Type and historically important specimens of 46 species and infraspecific taxa from Batrachospermum sect. Batrachospermum were examined. Of these, 48 specimens of 33 taxa were compared using multivariate morphometrics and image analysis. Nine species from the cluster analysis and one other species are recognised: B. anatinum, B. arcuatum, B. boryanum, B. carpocontorum, B. confusum, B. fluitans, B. gelatinosum, B. heterocorticum, B. pulchrum and B. skujae. B. ectocarpum is considered to be synonymous with B. anatinum, rather than with B. boryanum or B. arcuatum as has been proposed by previous authors. The illegitimately named species B. helminthosum Sirodot (non Bory) is referable to B. confusum as are B. crouanianum and B. fruticulosum. No varieties of B. gelatinosum could be supported and numerous taxa including B. pyramidale, B. densum and B. decaisneanum are synonymised within this species. The taxa in sect. Batrachospermum are separated on the basis of whether they are monoecious or dioecious, carpogonium size, and the presence or absence of (I) spermatangia on the involucral filaments, (2) irregular cortication, (3) monosporangia, (4) well-curled fascicles and (5) secondary fascicles. Other qualitative characteristics previously used to separate taxa in this section, such as carposporophyte position, hourglass-shaped cells of the carposporophyte-bearing branch and brown cortication, were found to be too variable for use as taxonomic criteria. Additionally, the quantitative characteristics overlapped among specimens and were only useful in distinguishing B. fluitans from B. anatinum. Revised descriptions and a synoptic key of the species are provided.