The genus Callinectes comprises seven species of blue crab found on the Brazilian coast, almost all are recorded in Cachoeira River estuary. The objective of this study is to analyse distribution of Callinectes species in the estuary of Cachoeira River (Ilhéus, Bahia). Monthly collections were conducted in the low tide of neap tide for a year and in five stations distributed according to the estuary salinity gradient. Six traps were assembled and submerged at each station for two hours. Sediment samples were collected for granulometric characterization and measuring of organic matter content. Temperature, salinity and pH were also measured in the bottom water, as well as water transparency at the start of each collection. Five species were collected: Callinectes danae, C. ornatus, C. exasperatus, C. larvatus and C. bocourti. The species presented different distribution patterns based on the salinity gradient and transversal profile of the estuary. Only C. danae was found in all collection points, and was the most abundant species throughout the study period. Callinectes ornatus was restricted to external estuarine areas, which presented higher salinity and transparency values. Callinectes larvatus predominantly occurred in the external station and estuary partitions, mainly in the margin. In spite of the occurrence of C. exasperatus throughout the entire estuary, this species was restricted to the margin. This study supports the assumption that species distribution patterns of this genus are the result of both variable influence, namely salinity, and complex intraspecific and interspecific relations between the congeneric species.