Frustules of Microcostatus are small in size. The axial area includes lyre-shaped depressions on both sides of the prominent sternum. The depressions contain small costae (microcostae) in a depression near the axial area. Striae are not typically visible with the light microscope. SEM reveals striae are present and comprised of single rows of areolae. In living cells, two plastids are present, pressed to the cingulum. The genus differs from Fallacia by the absence of a conopeum.
The genus includes species that belong to the former section Naviculae minusculae. The genus contains Microcostatus krasskei (Hust.) Johansen and Sray, M. naumanii (Hust.) Lange-Bertalot and M. maceria (Schim.) Lange-Bert., Kusber and Metzeltin, among other taxa. Microcostatus is typically found in aerophilous habitats, such as wet walls or moist soils.