| Genome Name | No of Superfamily |
| Fagonia cretica | 2 |
| Fagonia indica | 2 |
| Fagonia luntii | 2 |
| Fagopyrum callianthum | 2 |
| Fagopyrum cymosum | 2 |
| Fagopyrum esculentum | 6 |
| Fagopyrum gracilipes | 1 |
| Fagopyrum megacarpum | 2 |
| Fagopyrum pleioramosum | 2 |
| Fagopyrum sp. C97107 | 2 |
| Fagopyrum tataricum | 3 |
| Fagopyrum urophyllum | 2 |
| Fagraea sp. | 2 |
| Fagus crenata | 3 |
| Fagus grandifolia | 2 |
| Fagus japonica | 2 |
| Fagus sylvatica | 17 |
| Falcatifolium papuanum | 2 |
| Falcatifolium taxoides | 2 |
| Falco peregrinus | 1 |
| Falco sparverius | 1 |
| Falkia repens | 5 |
| Fallugia paradoxa | 2 |
| Faramea multiflora | 2 |
| Farfantepenaeus notialis | 1 |
| Fasciola gigantica | 3 |
| Fasciola hepatica | 12 |
| Fasciola sp. | 1 |
| Fatsia japonica | 2 |
| Fedia cornucopiae | 2 |
| Fejervarya cf. limnocharis | 1 |
| Fejervarya syhadrensis | 1 |
| Feldmannia irregularis | 2 |
| Feldmannia sp. virus | 3 |
| Felicia bergeriana | 2 |
| Feline calicivirus | 1 |
| Feline endogenous virus | 1 |
| Feline foamy virus | 2 |
| Feline herpesvirus 1 | 7 |
| Feline immunodeficiency virus | 12 |
| Feline infectious peritonitis virus | 1 |
| Feline leukemia provirus | 1 |
| Feline leukemia virus | 6 |
| Feline papillomavirus | 3 |
| Feline sarcoma virus | 5 |
| Feline syncytial virus | 2 |
| Felipponea esquirolii | 3 |
| Felis catus | 92 |
| Feltia jaculifera | 2 |
| Fendlera rupicola | 5 |
| Fendlerella utahensis | 4 |
| Fennellomyces linderi | 1 |
| Fenneropenaeus chinensis | 1 |
| Feralia major | 2 |
| Feretia aeruginescens | 2 |
| Fernelia buxifolia | 2 |
| Ferraria crispa | 3 |
| Ferraria uncinata | 2 |
| Ferroglobus placidus | 2 |
| Ferroplasma acidarmanus | 318 |
| Fervidobacterium islandicum | 6 |
| Fervidobacterium pennivorans | 5 |
| Festuca rubra | 1 |
| Festucopsis festucoides | 3 |
| Festucopsis serpentini | 3 |
| Fibrobacter intestinalis | 1 |
| Fibrobacter succinogenes | 11 |
| Ficalhoa laurifolia | 3 |
| Ficinia gracilis | 2 |
| Ficinia sp. Muasya 1233 | 2 |
| Ficinia striata | 3 |
| Ficus carica | 2 |
| Ficus pretoriae | 1 |
| Ficus sp. Soltis s.n. | 4 |
| Filarum manserichense | 2 |
| Filipendula purpurea | 2 |
| Filipendula vulgaris | 2 |
| Filobasidiella neoformans | 43 |
| Filobasidium floriforme | 1 |
| Fimbristylis complanata | 3 |
| Fimbristylis dichotoma | 3 |
| Finegoldia magna | 2 |
| Firmiana platanifolia | 2 |
| Fischerella sp. | 3 |
| Fischerella sp. PCC 7603 | 1 |
| Fischerella sp. UTEX 1931 | 1 |
| Fissidens adianthoides | 2 |
| Fissidens bushii | 2 |
| Fissidens dubius | 3 |
| Fissidens mooreae | 3 |
| Fissidens osmundoides | 2 |
| Fissidens philonotulus | 3 |
| Fissidens subbasilaris | 3 |
| Flabellaria paniculata | 2 |
| Flacourtia jangomas | 4 |
| Flacourtia montana | 2 |
| Flagellaria indica | 6 |
| Flammeovirga aprica | 1 |
| Flammulina velutipes | 5 |
| Flaveria anomala | 1 |
| Flaveria australasica | 1 |
| Flaveria bidentis | 9 |
| Flaveria brownii | 5 |
| Flaveria chloraefolia | 1 |
| Flaveria cronquistii | 1 |
| Flaveria linearis | 1 |
| Flaveria palmeri | 2 |
| Flaveria pringlei | 11 |
| Flaveria pubescens | 1 |
| Flaveria ramosissima | 1 |
| Flaveria trinervia | 10 |
| Flavescence doree phytoplasma | 2 |
| Flavobacterium aquatile | 1 |
| Flavobacterium ferrugineum | 6 |
| Flavobacterium johnsoniae | 12 |
| Flavobacterium keratolyticus | 2 |
| 'Flavobacterium' lutescens | 2 |
| Flavobacterium sp. | 7 |
| Flavobacterium sp. ATCC 21588 | 1 |
| Flavobacterium sp. SC12154 | 1 |
| Flavobacterium sp. SK1022 | 2 |
| Flavobacterium sp. U-188 | 2 |
| Flectobacillus major | 1 |
| Fletcherodrilus sigillatus | 2 |
| Fletcherodrilus unicus | 1 |
| Flexamia areolata | 2 |
| Flexibacter aggregans | 1 |
| Flexibacter elegans | 1 |
| Flexibacter flexilis | 1 |
| Flexibacter litoralis | 1 |
| Flexispira rappini | 1 |
| Flexistipes sinusarabici | 2 |
| Flickingeria fugax | 2 |
| Flindersia australis | 2 |
| Flintiella sanguinaria | 2 |
| Flock house virus | 1 |
| Floerkea proserpinacoides | 4 |
| Florometra serratissima | 1 |
| Floscopa scandens | 2 |
| Fluoribacter bozemanae | 2 |
| Fluoribacter dumoffii | 1 |
| Fluoribacter gormanii | 2 |
| Foeniculum vulgare | 2 |
| Foetidia asymetrica | 2 |
| Fokienia hodginsii | 1 |
| Folsomia candida | 3 |
| Fomitopsis cf. rosea | 2 |
| Fontinalis antipyretica | 3 |
| Fontinalis dalecarlica | 3 |
| Foot-and-mouth disease virus | 4 |
| Foot-and-mouth disease virus A | 3 |
| Foot-and-mouth disease virus Asia 1 | 2 |
| Foot-and-mouth disease virus C | 4 |
| Foot-and-mouth disease virus O | 7 |
| Foot-and-mouth disease virus SAT 1 | 2 |
| Foot-and-mouth disease virus SAT 2 | 3 |
| Foot-and-mouth disease virus SAT 3 | 2 |
| Fordia cauliflora | 1 |
| Forficula auricularia | 1 |
| Forficula decipiens | 1 |
| Forficula lesnei | 1 |
| Forgesia racemosa | 2 |
| Formicaphagus sp. KPJ-2001 | 1 |
| Formicaricola analoides | 1 |
| Formicarius colma | 2 |
| Formicarius nigricapillus | 1 |
| Forsstroemia japonica | 2 |
| Forsstroemia neckeroides | 2 |
| Forsstroemia trichomitria | 3 |
| Forstera bellidifolia | 5 |
| Forstera bidwillii | 2 |
| Forstera mackayi | 2 |
| Forstera sedifolia | 2 |
| Forstera tenella | 2 |
| Forsythia x intermedia | 4 |
| Fortunearia sinensis | 2 |
| Fortunella australis | 3 |
| Fortunella crassifolia | 1 |
| Fortunella japonica | 2 |
| Fossombronia foveolata | 2 |
| Fouquieria columnaris | 5 |
| Fouquieria sp. Anderberg s.n. | 3 |
| Fouquieria splendens | 1 |
| Four Corners hantavirus | 1 |
| Fowl adenovirus 12 | 1 |
| Fowl adenovirus A | 4 |
| Fowl adenovirus B | 1 |
| Fowl adenovirus C | 2 |
| Fowl adenovirus D | 4 |
| Fowl adenovirus E | 1 |
| Fowlpox virus | 22 |
| Fragaria vesca | 7 |
| Fragaria x ananassa | 41 |
| Franciella spiridentoides | 2 |
| Francisella philomiragia | 1 |
| Francisella tularensis | 19 |
| Francoa appendiculata | 2 |
| Francoa sonchifolia | 2 |
| Francolinus afer | 1 |
| Francolinus coqui | 1 |
| Francolinus erckelii | 1 |
| Francolinus francolinus | 1 |
| Francolinus pondicerianus | 2 |
| Frangipani mosaic virus | 1 |
| Frangula alnus | 1 |
| Frankenia hirsuta | 2 |
| Frankenia jamesii | 2 |
| Frankenia johnstonii | 2 |
| Frankenia pauciflora | 2 |
| Frankenia persica | 2 |
| Frankenia pulverulenta | 5 |
| Frankenia salina | 2 |
| Frankenia serpyllifolia | 2 |
| Frankia alni | 5 |
| Frankia sp. | 4 |
| Frankia sp. ACN14a | 1 |
| Frankia sp. ACN14a-tsr | 2 |
| Frankia sp. EuIK1 | 10 |
| Frankia sp. FaC1 | 1 |
| Frankia sp. Mrp182 | 2 |
| Franklandia fucifolia | 3 |
| Franklinia alatamaha | 2 |
| Frankliniella occidentalis | 1 |
| Frateuria sp. ANA-18 | 6 |
| Freesia alba | 2 |
| Freesia sp. 'Lejeune 1997' | 1 |
| Fremontodendron californicum x Fremontodendron mexicanum | 3 |
| Fremontodendron mexicanum | 2 |
| Fremyella diplosiphon | 16 |
| Freycinetia scandens | 5 |
| Friend mink cell focus-forming virus | 1 |
| Friend murine leukemia virus | 2 |
| Friend spleen focus-forming virus | 1 |
| Fringilla coelebs papillomavirus | 3 |
| Fringilla montifringilla | 2 |
| Fritillaria agrestis | 12 |
| Fritillaria cirrhosa | 1 |
| Fritillaria koidzumiana | 2 |
| Fritillaria liliacea | 1 |
| Fritillaria raddeana | 2 |
| Froelichia floridana | 2 |
| Frog adenovirus 1 | 5 |
| Frontiniella parancilla | 1 |
| Frontiniella regilla | 1 |
| Frontonia sp. | 2 |
| Frullania dilatata | 1 |
| Frullania polysticta | 1 |
| Frullania tamarisci | 1 |
| Fuchsia cyrtandroides | 2 |
| Fuchsia hybrid cultivar | 1 |
| Fuchsia procumbens | 2 |
| Fucus distichus | 5 |
| Fucus serratus | 1 |
| Fucus vesiculosus | 6 |
| Fuirena ciliaris | 3 |
| Fuirena sp. Thomas et al. 10404 | 2 |
| Fuirena welwitschii | 2 |
| Fujinami sarcoma virus | 4 |
| Fulica atra | 1 |
| Fulicoffula heliornis | 1 |
| Funalia trogii | 1 |
| Funaria apophysata | 3 |
| Funaria hygrometrica | 7 |
| Fundulus heteroclitus | 16 |
| Fundulus parvipinnis | 2 |
| Funiculina quadrangularis | 2 |
| Funtumia elastica | 2 |
| Furcellaria lumbricalis | 1 |
| Furcraea gigantea | 1 |
| Furcula cinerea | 3 |
| Furculomyces boomerangus | 2 |
| Furnarius cristatus | 1 |
| Furnarius rufus | 2 |
| Fusarium bactridioides | 4 |
| Fusarium begoniae | 1 |
| Fusarium beomiforme | 1 |
| Fusarium buharicum | 1 |
| Fusarium cerealis | 2 |
| Fusarium concolor | 1 |
| Fusarium culmorum | 2 |
| Fusarium dlaminii | 1 |
| Fusarium equiseti | 3 |
| Fusarium inflexum | 1 |
| Fusarium lateritium | 1 |
| Fusarium lichenicola | 1 |
| Fusarium lunulosporum | 2 |
| Fusarium napiforme | 1 |
| Fusarium oxysporum | 36 |
| Fusarium oxysporum f. sp. ciceris | 3 |
| Fusarium oxysporum f. sp. lycopersici | 7 |
| Fusarium oxysporum f. sp. radicis-lycopersici | 1 |
| Fusarium poae | 1 |
| Fusarium proliferatum | 5 |
| Fusarium pseudograminearum | 1 |
| Fusarium pseudonygamai | 1 |
| Fusarium sacchari | 1 |
| Fusarium solani | 3 |
| Fusarium sp. | 1 |
| Fusarium sp. NRRL22903 | 1 |
| Fusarium sp. NRRL 25195 | 1 |
| Fusarium sp. NRRL 25204 | 1 |
| Fusarium sp. NRRL 25309 | 1 |
| Fusarium sp. NRRL 25346 | 1 |
| Fusarium sp. NRRL 25623 | 1 |
| Fusarium sp. NRRL 26427 | 1 |
| Fusarium sporotrichioides | 2 |
| Fusarium subglutinans | 2 |
| Fusarium venenatum | 1 |
| Fusobacterium mortiferum | 4 |
| Fusobacterium nucleatum | 506 |