ABSTRACT Macrobrachium acanthurus is an amphidromous palaemonid shrimp exploited by artisanal fishing in Brazil that presents limited published information on its population biology. Therefore, this study aimed to assess the spatial distribution and fecundity of M. acanthurus in the Jequitinhonha River (BA). Collections occurred at four points in the river downstream of the Itapebi Hydroelectric Powerplant (P1–P4). The abundance and size of the demographic categories analysed (male morphotypes, non-ovigerous females, and ovigerous females) and fecundity were compared among points. We also examined the relationship between female body size and fecundity. A total of 938 individuals were collected during the sampling period. The highest abundances were observed downstream (P3 and P4). The sizes of males and ovigerous females were greater at points farthest upstream. Three male morphotypes were identified, and their proportions varied among points. Fecundity was higher upstream, and there was a positive correlation between female size and number of eggs. All population parameters indicate a longitudinal gradient towards the estuary, with strong evidence of amphidromy. This is the first study with a polymorphic species to consider morphotypes as a population structure component. The results represent an important contribution to a better understanding of the amphidromous life cycle of palaemonid shrimp.