Fragmentation reduces habitat area, increases the number of habitat patches, decreases their size, and increases patch isolation. For arboreal mammals such as howlers (Alouatta palliata), canopy modifications from fragmentation processes could also negatively affect habitat quality. We analyzed changes in the composition and plant structure of 15 fragments (1–76 ha) and compared them with vegetation from a continuous tropical rain forest reserve (700 ha) in Los Tuxtlas, Mexico. At each site, we sampled 1000 m2 of all trees, shrubs, and lianas with a diameter at breast height (DBH) ≥10 cm. We obtained estimates of species richness, density, and basal area for different ecological groups, DBH ranges, and top food resources for howlers. We used a stepwise multiple regression analysis to determine relationships between fragment characteristics (size, shape index, and isolation) and plant variables. Compared to continuous forest, fragments have altered composition and plant structure, with large trees absent from the canopy. The basal area of top food resources is higher in continuous forest. Fragment size is the best explanation for the differences in composition and plant structure. The largest fragments had greater basal area of top food resources and more large primary trees in the canopy. Overall, our results suggest that fragmentation altered the habitat quality for howlers.