We used a microsatellite-enriched library to isolate and characterize 16 di-nucleotide microsatellite loci in Semaprochilodus insignis. Microsatellites were characterized in a population sample from Piagacu-Purus (Purus River, Amazonas, Brazil) and in eight individuals each of S. brama from Itaipavas (Araguaia River, Para, Brazil), S. taeniurus from Novo Airao (Negro River, Amazonas, Brazil), S. kneri (Caura River, Venezuela), and Prochilodus nigricans also from Piagacu-Purus. In S. insignis observed heterozygosities ranged from 0.516 to 0.968, expected heterozygosities from 0.574 to 0.973, and the number of alleles per locus varied from 4 to 32 in 31 analyzed individuals. All loci were unlinked and three loci showed significant deviations from Hardy–Weinberg equilibrium. Most markers could be successfully transferred to the other four prochilodontids, making them potentially useful for conservation genetic studies of Semaprochilodus spp.