The distribution and feeding ecology of two puffer fish, Sphoeroides testudineus (Linnaeus, 1758) and Colomesus psittacus (Bloch & Schneider, 1801), were investigated in a tropical estuary (north-eastern Brazil). The hypothesis tested was that these two species partition available resources spatially, and that the effects of interspecific competition can be reduced by changes in the feeding strategy and using alternative resources. This study was carried out between February 2011 and January 2012, on a beach and three tidal creeks of the Mamanguape River estuary. Data on the distribution and relative abundance of the two species were collected using beach seine, with data on temperature, salinity and turbidity also recorded. The diets of the species (S. testudineus N = 399; C. psittacus N = 108) were analysed by the Index of Relative Importance (IRI). Sphoeroides testudineus was found in the entire area, but was particularly abundant in the upper estuary, while C. psittacus was captured exclusively in the upper estuary, with all individuals assumed to be juveniles. In regard to feeding, juvenile S. testudineus predated on Bivalves, Ceratopogonidae larvae, calanoids and gastropods; whilst C. psittacus showed a diet more specialized in Brachyura and Cirripedia. These results suggest that there are differences in both habitat utilization and feeding habits of these two puffer fish species in this estuary.