Mechanisms related to ecological or sexual selection have favoured sympatric speciation events in African and Central American lake cichlids. Allopatric divergence is the predominant speciation process observed in Amazonia, although, to the best of our knowledge, no study to date has attempted to determine whether speciation process could exist under sympatric conditions in Amazonian cichlids. The Apistogramma agassizii species complex is an excellent model for investigating the existence of sympatric divergence events in the Amazon, as it shares many common life history characteristics with African Haplochromine cichlids in which sympatric speciation mechanisms are well documented. The genetic structure of A. agassizii was analysed by genotyping 889 individuals with ten microsatellite loci, collected from 26 sites distributed among small streams in 11 micro-basins in a very small portion of the Peruvian Amazon. It revealed 22 genetic populations identified according to panmictic criteria (FIS estimator) and strongly differentiated: FST estimator (0.034 to 0.356). Such a strong genetic structuring on such small geographical areas has never been demonstrated before in an Amazonian fish. Several of these populations may have diverged sympatrically and repeatedly in small stream networks. The results are discussed with respect to divergence processes, including sympatric speciation, that may be associated with the observed genetic structure.