Simpsonichthys nigromaculatus, new species, collected in a seasonal swamp at the floodplains of rio da Prata, rio Aporé drainage, upper rio Paraná basin, central Brazil, is described. It is a member of the western clade of the subgenus Simpsonichthys, which is diagnosed by having 24-26 vertebrae, a dark gray band bordered by a bright blue line on the margins of the unpaired fins in males, the anterior and posterior margins of the iris bright blue, a maximum adult size about 25 mm SL, and by the absence of pelvic fin and pelvic girdle, and second pharyngobranchial teeth; this clade also includes S. parallelus and S. cholopteryx. Simpsonichthys nigromaculatus is hypothesized to be more closely related to S. parallelus by both species sharing the presence of a short postorbital pink stripe and the basal portion of all unpaired fins orange in males. It further differs from S. cholopteryx by having fewer anal-fin rays in females, narrower blue bars on flank in males, and absence of bars on fins; and from S. parallelus by having yellow dots on the caudal fin in males and deeper body in males.

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