Gomphonema abbreviatum- Gomphonema acuminatum
- Gomphonema affine
- Gomphonema ampullaceum
- Gomphonema angusta
- Gomphonema angustatum
- Gomphonema anomalum
- Gomphonema augur
- Gomphonema carolinense
- Gomphonema cholnokyites
- Gomphonema commune
- Gomphonema cristatum
- Gomphonema curvirostrum
- Gomphonema dichotomum
- Gomphonema elongatum
- Gomphonema flabellatum
- Gomphonema fulgens
- Gomphonema fusticulus
- Gomphonema geminatum
- Gomphonema gracile
- Gomphonema hatherlianum
- Gomphonema hebridense
- Gomphonema herculeana
- Gomphonema hyalinum
- Gomphonema incognitum
- Gomphonema insigne
- Gomphonema intricatum
- Gomphonema irremedia
- Gomphonema italicum
- Gomphonema kasnakowi
- Gomphonema lagenula
- Gomphonema leibleini
- Gomphonema lenormandi
- Gomphonema martini
- Gomphonema micropus
- Gomphonema minustissimum
- Gomphonema minutissimum
- Gomphonema minutum
- Gomphonema montanum
- Gomphonema montezumense
- Gomphonema naviculoides
- Gomphonema nediense
- Gomphonema nepalensis
- Gomphonema nipponica
- Gomphonema olivaceum
- Gomphonema pachycladum
- Gomphonema paradoxum
- Gomphonema pararhombicum
- Gomphonema parvulum
- Gomphonema pohliaeforme
- Gomphonema productum
- Gomphonema pseudotenellum
- Gomphonema ramosum
- Gomphonema robustum
- Gomphonema rostratum
- Gomphonema sarcophagus
- Gomphonema sinestigma
- Gomphonema sphaerophorum
- Gomphonema subacaule
- Gomphonema subclavatum
- Gomphonema submehleri
- Gomphonema subramosum
- Gomphonema subtile
- Gomphonema tenue
- Gomphonema tholus
- Gomphonema truncatum
- Gomphonema turris
- Gomphonema varioreduncum
- Gomphonema ventricosum
- Gomphonema vibrio
- Gomphonema zairense