This taxon was historically associated with B. procera, however upon inspecting the type material of B. microcephala, Van de Vijver et al. (2021) concluded that the type of B. procera belongs within the upper size range of B. microcephala.
Brachysira brebissonii, B. microcephala, and B. confusa are isopolar.
Brachysira ocalanensis has linear valve margins (from center of the valve to the apices)(Shayler and Siver 2004).
Brachysira vitrea has striae that are often not resolved in LM (see Van de Vijver et al. 2023).
Brachysira subtilis has more broadly rounded apices.
Brachysira neoexilis has capitate apices.