In Mexico, shrimp is the most important fishing resource in terms of value, and second in production. Ten percent of the country's production comes from catches in the southern Gulf of Mexico. Several studies report the number of marine species recorded in this zone; however, few consider bycatch, and still fewer determine biodiversity indexes. This work identified the species captured in shrimp trawls from 22 commercial fishing trips from August 2016 to December 2017 in the south of the Gulf of Mexico. Four indexes of taxonomic diversity were determined: richness, evenness, average taxonomic distinctness, and variation. The indexes were calculated by season (dry, rainy, and northerly), spatial scale (terrigenous, carbonate, and Contoy zones), and depth interval: 1 (<10 m), 2 (10-20 m), 3 (20-40 m), and 4 (>40 m). The zones were separated according to the sedimentological characteristics described in the literature, and the depth ranges were arbitrarily defined considering the bathymetry of the zone. Nine classes, 51 orders, 121 families, 207 genera, and 334 species (152 terrigenous, 289 carbonates, and 76 Contoy) were recorded. Evenness index was highest in Contoy (0.75), followed by the terrigenous (0.54) and carbonate zones (0.35). Average taxonomic distinctness was greater in the carbonate (83.51) zone, followed by the Contoy (75.83) and terrigenous (74.55) zones. Contoy was identified as the most variable based on taxonomic distinctness (301.1). Also, the same index calculated by depth stratum and zone showed that the deeper zones generally have more phylogenetic relationships. The determinations of these indexes are proposed and can be used as points of reference to assess the variation and status of marine communities in the region.