Stems absent or less than 1 mm, but up to 3.7 mm in M. synoicum. Leaves usually somewhat shriveled or contorted when dry; costa commonly none, but occasionally suggested by a few median cells with thick walls or by a short and indistinct double layer beyond the middle; laminal cells lax, hyaline, non-papillose. Sexual condition synoicous or dioicous. Capsule cleistocarpous or dehiscing along a ring of differentiated cells at or distal to the equator, globose or subglobose, without a multicellular apiculus, less than 0.4 mm from base to apex; exothecium of 1-2 cell layers; columella absent in maturing capsules. Calyptra persistent, minute, scarcely more than the remnants of the archegonial venter and neck, tightly adherent at or near the capsule apex, less than 0.16 mm.

Micromitrium differs from Ephemerum in having a persistent, minute calyptra, consisting of merely the archegonial neck and distal portion of the venter, a capsule that is globose and regularly dehiscent in most species, usually ecostate leaves with leaf cells that are large, hyaline, and non-papillose. Except for M. megalosporum and M. wrightii, Micromitrium differs also in having an operculum (though rudimentary), no spore sac, and no stomates. Micromitrium megalosporum and M. wrightii resemble Ephemerum in having a usually cleistocarpous capsule, an exothecium of two layers, and stomates. Cytological characters confirm the distinctness of the two genera. At the time of meiosis Micromitrium capsules are remarkably smaller than mature capsules, while capsules of Ephemerum, at the time of meiosis, are approaching their mature size. A difference in size is also seen in the spore mother cells undergoing meiosis: in the species of Micromitrium that have been studied cytologically, M. tenerum (as Nanomitrium austinii) and M. megalosporum (as N. megalosporum), the spore mother cells are very small and include 10, 11, or 22 chromosomes, in comparison with the large spore mother cells of Ephemerum with 27 chromosomes (V. S. Bryan 1957). In the latter, meiotic chromosome configurations occupy only a small volume of the large spore mother cells.