Tropical forests are subject to increasing pressures due to global change. Globally, tropical dry forests (TDFs) have been heavily impacted and these impacts have been poorly quantified. Despite its large coverage in tropical regions, and its important influence on the global C cycle, little is known of spatial variations in aboveground biomass (AGB) distribution of TDFs. The understanding of TDF aboveground biomass has been biased towards the secondary forests, with few studies of mature forests. The aim of this study is to quantify, allocate and understand the natural factors responsible for driving the AGB distribution and, consequently, on C stocks, in natural TDFs in Mexico. The study region represents ∼14% of the total TDF area in Oaxaca. Remote sensing time series across field sites were used to identify suitable sampling locations for mature forests in Oaxaca. Aboveground biomass was normally distributed with a mean of 117 ± 5 Mg ha−1 (±1 SE). Large trees (diameter at breast height, DBH ≥ 30 cm) were found at similar frequencies in small (300–400 m2) and large (4 ha) plots. Depending on the selected allometric equation, at least 60% of the AGB is held in trees with DBH < 28.7 cm. At local scale, large trees (DBH ≥ 30 cm) did not show spatial autocorrelation and, in the landscape, AGB showed a spatial correlation in distances < 250 m. Because of low densities of very large trees (DBH ≥ 75 cm), the mean AGB estimates across different allometric equations only resulted in differences of ∼10%. State factors including climate (mean annual precipitation, temperature and solar radiation) and topography (altitude and distance to streams) modulate the TDF structure and its potential for aboveground storage C across the landscape. Soil texture and pH were the most important soil properties in explaining variations in AGB, with stronger effects than soil nutrients. Across different scales of analysis, higher biomass estimates were related to water availability. This information can support spatial estimates of biomass storage capacity for Mexican TDF, crucial for land and C management.