Cattle and agricultural farming in the western Orinoco Basin began in 1555, and since then fragmentation of continuous forest has occurred. We evaluated the effects of the disturbances and the absence of large primates on plant community composition, diversity, and regeneration patterns. Atelines (Lagothrix and Ateles) inhabited the lowlands close to the Andean mountains, but no longer live in fragmented habitats. Their absence may have negative effects on plant populations because atelines play important roles as seed dispersers in neotropical forests, especially for large-seeded plants, which are rarely swallowed by other seed dispersers. We compared 2 1-ha vegetation plots in forest fragments north of the La Macarena Mountains with 7 plots in continuous forest in Tinigua National Park. Both sites share the same climatic conditions and have similar geological origins. There is floristic affinity between forests with similar ecological characteristics; the fragmented forests are also less diverse than the continuous forests. As predicted, the forest fragments have fewer individuals with large seeds. The results suggest that forest fragmentation and local ateline extinctions affect plant communities, reducing diversity and affecting large-seeded plants.