Astyanax scabripinnis, a small neotropical freshwater fish, is a headwater species living in small tributaries of many Brazilian rivers, where they form isolated populations. This species harbors a B chromosome system in several populations. Among the several kinds of Bs reported in this species, the BM variant, a large metacentric of a similar size to the largest A chromosome, is the most widespread in natural populations. It probably corresponds to the ancestral B type in this species and a very similar B chromosome is also found in other Astyanax species. Strong evidence suggests that this B is an isochromosome showing structural and functional homology between its two arms, as shown by satellite DNA localization and the formation of a ring B univalent during meiosis. The BSM and Bm variants, a large submetacentric and a small metacentric, respectively, represent rare variants and may be derived from structural rearrangements of the BM chromosome. In addition, B microchromosomes (Bmicro) were found in some populations. Frequency analyses in mountain populations have shown that B chromosomes are found in populations located at high altitude, but are absent in populations at low altitude, which is consistent with their parasitic nature, given the ecological peculiarities of both kinds of populations.