Neostethus geminus is most closely related to N. bicorni. Both species differ from all congeners by having two elongate curved ctenactinia (vs. one elongate and one short ctenactinium) in mature males and a brown blotch on the pelvic-fin rays of the proctal side of immature males, and a fleshy, hood-like fold in females that includes the anus and genital and urinary pores. Neostethus geminus is distinguished from N. bicornis in being smaller (reaching no more than 2.57 cm SL vs. 3.1cm SL), and having a relatively compact priapium with a foreshortened, broad aproctal axial bone that meets but does not overlap the pulvinular appendage (vs. a relatively elongate priapium with a long and narrow aproctal axial bone that overlaps the pulvinular appendage medially); thin, nearly translucent, broad papillary bone expanded distally into a tab (vs. a short papillary bone), and females with a thickened fleshy, hood-like fold that includes the anus, genital pore and urinary pore (vs. a thin fold of skin), and a thickened ridge just posterior to the fold and separated from it by a gap (vs. lacking a ridge and a gap) (Ref. 95599).