Abstract
Seasonally dry tropical forests (SDTF) host ecologically distinct vegetation types, with differences in forest structure, taxonomic diversity, and aboveground carbon stocks that remain insufficiently quantified. We compared a semi-evergreen tropical forest (SETF) and a seasonally flooded lowland forest (SFLF) in the Calakmul region of south-eastern Mexico. A total of 2,622 trees were recorded across 10 plots (40 subplots;
n
= 20 per type), measuring forest structure parameters such as basal area, canopy height, and clear bole height. We estimated above-ground carbon stocks, taxonomic diversity (Hill’s q0–q2 indices using iNEXT rarefaction/extrapolation), and floristic composition (NMDS, PERMANOVA). Basal area, canopy height, and carbon stocks were significantly higher in SETFs (33.4 m
2
ha
−1
, 15.3 m, 118.9 t C ha
−1
) compared to SFLFs (24.1 m
2
ha
−1
, 11.5 m, 63.6 t C ha
−1
), while stem density showed no difference between the two. A linear mixed model explained 97.4% of the variance in carbon stocks (marginal
R
2
= 0.974), with basal area as the strongest single predictor (semi-partial
R
2
= 0.255), partly reflecting the shared allometric basis of basal area and carbon estimates. Leaf area index made no independent contribution, suggesting that seasonal flooding reduces carbon storage primarily through smaller individual stem size rather than differences in stand density or canopy cover. Contrary to our prediction, Shannon and Simpson diversity indices were significantly higher in the SFLF at a standardised sample size, indicating that periodic flooding reduces competitive dominance and promotes more equitable abundance distributions, rather than decreasing species richness. Floristic composition differed entirely between the two types (PERMANOVA
R
2
= 0.73). Given projected drought trends for the Yucatán Peninsula, shifts in flooding seasonality could drive landscape-scale carbon losses that low-resolution global models may miss. These findings underscore the ecological importance of seasonally flooded forests and the risk of systematically undervaluing them in carbon-based conservation strategies.