This study aimed to identify alterations in gills and hepatopancreas of the crab Ucides cordatus as indicative of environmental contamination in mangrove areas subject to chemical effluents from port activities in Maranhão, Brazil. Samples of gills and hepatopancreas were removed from each animal and fixed in Davidson's solution until the procedure of histological technique. The biometric data (means and standard deviations) of the specimens collected in the study areas indicated that the crabs in the reference area are significantly (P < 0.05) higher and heavier than the crabs collected in the potentially impacted area (port area). Gill alterations (rupture of pilaster cells, dilation of the marginal channel, cuticle rupture and necrosis) and hepatopancreas alterations (abnormal lumen, vacuolized B cells, pycnotic nuclei and necrosis) were significantly (gbn < 0.05) more frequent in crabs collected in the port area than crabs collected in the reference area. These data indicate that the health of crabs is compromised due to the pollutants present in the mangroves that surround the port area in São Marcos’ Bay.