Acanthocephalan parasites, specifically from the genus Profilicollis, are known to infect decapod crustaceans, including mole crabs like Emerita brasiliensis, which serve as intermediate hosts in their complex life cycles. This study reports the first occurrence of the acanthocephalan parasite Profilicollis altmani infecting the mole crab Emerita brasiliensis on a sandy beach in southeastern Brazil, thereby expanding the known geographic range of this parasite. Additionally, the study provides novel molecular data that enhance our understanding of the parasite’s taxonomy and distribution, including the first evidence of genetic variation within populations of the intermediate host E. brasiliensis. Phylogenetic analysis based on mitochondrial COX1 gene sequences confirmed the identification of the parasite and underlined small genetic differences among P. altmani populations. These findings suggest a weak genetic population structure of the parasite and underscore the need for further studies to understand gene flow among these populations. This work contributes to the knowledge of parasite-host interactions in sandy beach ecosystems. It highlights the importance of monitoring parasitic infections in species like E. brasiliensis, which play a crucial ecological role in these environments.