The silver and black croakers, Plagioscion squamosissimus and P. auratus respectively, are fishes belonging to the Sciaenidae family inhabiting South America freshwaters drainages, occurring in simpatry in the Amazonian flood plain. Morphologically, both species are validated, however, recent studies revealed a complete similarity between species at the COI mitochondrial DNA and the nuclear Tmo-4C4 DNA. Aiming to evaluate the taxonomic status of both species, as well as their genetic diversity and population structure, we evaluated 199 specimens, with 108 for P. squamosissimus and 91 for P. auratus at the Pará state cities such as Santarém, Alenquer, Juruti, Monte Alegre and Bragança. A partial fragment with 644 bp of the control region was analyzed from all the sampled specimens, and 432 bp of the nuclear Tmo-4C4 DNA for 40 individuals of P. squamosissimus and 30 specimens of P. auratus were compared. Phylogenetic trees, for the two markers, separate the two taxa in reciprocally monophyletic clades with high bootstrap values confirming the status of species for P. squamosissimus and P. auratus. Similarly, interspecific population analyses corroborate the maintenance of the taxa as distinct species. Interspecific analyses of the control region revealed that associating genetic diversity and demographic history, the populations of silver and black croakers of the medium Amazon region show typical patterns of stable populations with long evolutionary history. The population of black croaker from Bragança has passed through bottleneck due to a founder effect, which may have been produced by anthropic introduction at the Caeté estuary. The silver croaker is constituted for populations connected by gene flow mediated by females along of the main chanel of the Amazon River, as well as for black croaker which might be considered panmictic at the Medium Amazon region. The genetic differentiation of black croaker from Bragança in relation to the other populations of this species might be attributed to the random genetic drift promoted by the founder effect, once the sharing of haplotypes of this with populations from the Medium Amazon region suggest a origin from individuals from that area. Finally, the pattern of genetic homogeneity observed for the both species may be related to the flood pulses connecting lakes and tributaries of the main channel of the Amazon River during the period of high waters of Amazonian várzea. These results may be used for management plans of those two important fish resources at the Amazon region.
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