The genus Achirus is made up of demersal fish that have a close relationship with the substrate and exhibit peculiar aspects during their larval stage. The aim of the present study was to determine whether the abundance of Achirus larvae differed among a set of habitats in the estuary of the Formoso River in the State of Pernambuco (north-eastern Brazil). Sampling was performed monthly between April 2009 and March 2010, and comprised horizontal hauls with plankton net during the day and night in mangrove, beach and reef habitats. Fish larvae were sorted, identified, measured and larval stage recorded. Density and body length values were used in a non-parametric analysis of variance for the determination of variations between seasons, habitats and diel periods. A total of 204 larvae were collected, with an average density of 2.1 larvae.100 m−3. Density was greater in the nocturnal samplings, with no differences found between habitats. The larvae occurred in the yolk-sac to post-flexion stage, with pre-flexion the most abundant stage (78%). Size segregation was observed. Larger larvae were captured at night and in the mangrove. The smallest larvae were caught on the reef, with length increasing toward the mangrove. The results indicate that Achirus larvae come from deeper regions near reefs, where spawning probably occurs, and perform ontogenetic migration towards the shallow waters of mangrove, where they settle.