In this study we describe the morphological variation of Ischnocnema ramagii from a population sample within the Municipality of Salvador, Bahia State, Brazil, and characterize two extremely distinct morphotypes within this taxon (striped vs. non-striped dorsum); we describe its karyotype, and compare the karyotypic structure of the distinct morphotypes recognized herein. Specimens with striped dorsa were less common (13–18%) than those with non-striped dorsa (81–86%), the latter group comprising a mix of discrete color pattern states, whose frequencies were not different among juveniles, males, and females. The PCAs on morphometric data resulted in a strong degree of superposition between striped and non-striped dorsa, for both genders. We encountered a diploid number of 30 chromosomes for both males and females, with chromosome pairs 1 to 15 being telocentric. The karyotypic comparison between specimens with striped and non-striped dorsa did not show any noticeable difference. Nevertheless the karyotype of I. ramagii from Salvador, Bahia, differed from the karyotype described for I. paulodutrai from Ilhéus, Bahia, which showed a submetacentric chromosome pair. This result supports the presence of two full “sibling” species in Bahia State, one from the south (I. paulodutrai) and another from the north (I. ramagii), validating the identity of I. paulodutrai as a full species, and refuting the recognition of Salvador samples as I. paulodutrai. The high number of telocentric chromosomes suggests a closer relationship between I. ramagii and “Eleutherodactylinae” species from Central America and the northern region of Brazil.