The gametophytes of Schizymenium, Mielichhoferia and Pohlia are extremely similar, and the relationship between Schizymenium and Mielichhoferia is especially close. Mielichhoferia, with one exception, is a dioicous genus, and while most members of Schizymenium are paroicous or autoicous there are a few dioicous species. Both genera have reduced peristomes that can be either single or double. In Mielichhoferia the peristome when single is exostomial and when double consists of a fairly well-developed, usually papillose, exostome and an endostome reduced to little more than a basal membrane. In contrast, the peristome of Schizymenium when single is endostomial and when double consists of an often reduced, usually smooth exostome and a fairly well-developed endostome that has a basal membrane and long, filiform segments. Shaw et al. (1998) considered the dioicous species of Schizymenium with well-developed double peristomes (all restricted to tropical America) to be phylogenetically basal within the genus.

Most Pohlia species differ from Schizymenium in having a well-developed double peristome with striate exostome teeth and a fully developed endostome. There are, however, Pohlia species with reduced exostomes and endostomes as well as a few double peristome species of Schizymenium with exostome teeth that are morphologically similar to those in Pohlia (e.g., S. pseudopohlia Shaw). In such cases Pohlia can be distinguished from Schizymenium by its densely papillose-pitted rather than weakly papillose exostome teeth, and enlarged outer perichaetial leaves that are more strongly serrate, have stronger costae, and longer leaf cells than the vegetative leaves. In Schizymenium the perichaetial leaves are smaller than the vegetative leaves.

There are inherent taxonomic difficulties in working with a genus that has non-descript gametophytes and reduced peristomes because only well-developed material can be named with confidence. For example, in TENN there is a very small duplicate of a Costa Rican collection (Crosby 3636) with eroded, eperistomate capsules that has been annotated as S. clavellatum (Mitt.) Shaw, an eperistomate species from Colombia. The original collection in MO, however, has mature, operculate capsules with single, endostomial peristomes and is actually S. serratum.