The spatial distribution of Farfantepenaeus shrimp was analysed in the Laguna Madre of Tamaulipas, Mexico. Sampling was carried out on submerged aquatic vegetation (SAV) habitats at five sites located along the coastal lagoon. Two nocturnal surveys were conducted during winter in 2005 (January–February), collecting a total of 3268 shrimp individuals. SAV beds were composed of a mixture of drift algae (mainly Digenia simplex), attached algae (mainly Penicillus capitatus and Udotea occidentalis) and seagrass (mainly Halodule wrightii). Farfantepenaeus aztecus was more abundant (39.5%) than F. duorarum (36.8%), and the remaining 23.7% corresponding to small unidentified Farfantepenaeus spp. were classified as recruits. Abundance of F. aztecus was significantly higher at sites 2 and 4, whereas F. duorarum did not show significant distribution differences along the Laguna Madre. Recruits, juveniles and total shrimp tended to decrease significantly at the northern part of the lagoon (site 1), where substrate was dominated by drifting algae and seagrasses were scarce or absent. The abundance of shrimp was positively related to seagrass biomass and/or water temperature, whereas there was a negligible or negative relationship with algal biomass. With the exception of subadults, a significant positive linear relationship between seagrass and shrimp abundance was fitted, indicating an increase in number of individuals of both species with increasing seagrass biomass. This suggests that seagrass is the most important component of SAV beds influencing the abundance of F. aztecus and F. duorarum along this hypersaline coastal lagoon.