The effects of precipitation regime on the size of soil carbon (C) pools were compared in mature tropical dry forests of the Yucatan Peninsula. Our study included three forest stands in each, a dry site (potential evapotranspiration ratio = 3.2 mm mm−1; mean annual precipitation = 537 mm), a wetter site (2.0 mm mm−1; 993 mm) and a site in which water was comparatively less limiting (1.3 mm mm−1; 1086 mm). At each site, soil C pools in dead fallen phytomass (includes leaves, flowers, fruits, small twigs and deadwood debris) deposited on the litter layer and in roots and organic matter of the mineral soil (from the upper 10 cm) were measured in samples collected during the dry season. A high proportion of the total C pool (93–95%) was in the top 10 cm of soil in all forest sites. The smallest C pool was in roots (1.8–2.4% of the total C), meanwhile the C in the litter layer represented 3–5% of the total pool. These patterns were observed irrespective of study site. However, distribution of C (i.e. wood debris vs. fine litter) varied across sites; the proportion of the forest-floor C pool in wood debris decreased from 80% in the driest site, to 51% and 42% in 993-mm and 1086-mm sites, respectively. Overall, we observed that three pools (wood debris, roots and soil organic C) provide evidence for the significant decrease in soil C storage with increase in mean annual precipitation in Yucatan Peninsula. A potential explanation for this unexpected pattern includes an increasing C turnover time with decreasing mean annual precipitation, resulting in higher C accumulation per unit of C input in the driest site.