The Curimatidae family plays an ecological role in the recycling and distribution of nutrients and constitutes a major food source for several commercially important fishes. Curimata mivartii, a member of this family, is considered a short-distance migratory species (≤100 km), categorized by the International Union for Conservation of Nature as a near threatened species, based on its declining population densities and habitat disturbance and fragmentation. Since population genetics and species-specific molecular tools remain unknown for all members of the Curimatidae family, this study developed a set of microsatellite loci and studied the population genetics of C. mivartii in the lower section of the Colombian Magdalena-Cauca basin. The results showed high levels of genetic diversity and evidence of gene flow even between locations separated over 350 km. This information provides a baseline for designing conservation and management programs for C.mivartii and constitutes the first study of population genetics in Curimatidae.