In order to know and characterize the benthic marine community at Guerrero Negro Lagoon, Baja California Sur, Mexico, a monitoring during six months were conducted, sampling 10 stations every month from July to December of 2012. Collected samples were taken with 0,50 m(2) quadrants by scuba between 5 and 12 m in depth during periods of syzygy tides. All information was analyzed by ecological indicators and multivariate statistical analyzes. Our results showed that marine benthic community is represented by 229 species corresponding to 11 phylum, highest species richness was represented by mollusks (95 species), and the most abundant was arthropods group (7543 individuals). Ecological indicators denoted similar patterns in the time domain except for July, with the lowest value for richness (S = 88) compared with (S) over bar = 105 for the other months; and high heterogeneity in the spatial domain, finding statistical differences in the ecological indicators values between sampling stations. Considering spatial high heterogeneity, we performed a multidimensional scaling analysis finding two assemblages (groups A and B). Group A includes stations associated with secondary channels of the lagoon, lower current strength and with less oceanic influence, and in which case, be denoted ecological indicators mostly rich and diverse; while Group B consists of the stations located in the main channel of the lagoon, with more dynamic currents and high oceanic influence, suggesting a permanent space stratification mainly influenced by the dynamic current patterns of the lagoon.