BackgroundSemaprochilodus insignisis a migratory fish of commercial and subsistence importance to communities in the Amazon. Despite the high intensity of exploitation, recent studies have not been carried out to assess the genetic status of its stocks.MethodsThis study is the first to estimate genetic diversity and to test the existence of spatial and temporal structuring ofS. insignisthrough sequencing of the mtDNA control region (n= 241) and eight microsatellite loci (n= 180) of individuals sampled at 11 sites distributed in the Brazilian Amazon basin.ResultsResults for both markers were congruent, revealing a homogeneous genetic diversity in all the sampled locations, in addition to the absence of spatial and temporal genetic structure, indicating that the species forms a large panmictic population in the Brazilian Amazon.DiscussionAlthough overfishing does not yet appear to have affected the levels of genetic variability ofS. insignis, signals of reduction of the effective population size and a bottleneck provide an early alert to the effects of overfishing. Thus, the ever-decreasing populations may threatenS. insignisin the future. Therefore, it is hoped that the results of this study may contribute to the elaboration of management plans or any other measures that aim at the management and conservation of this species of great importance for the Amazon basin.