Agricultural activity associated with habitat conversion is a major driver of biodiversity loss across the tropics. The decline of species richness is a common outcome of conversion to agricultural land-use, but the associated changes in functional and phylogenetic diversities, and spatial patterns of beta-diversity, are not well understood. Here we investigate the effects of conversion to rubber plantation on ant taxonomic, functional and phylogenetic diversities at local and among-sites scale in Southeast China. We found a sharp decline of ant species richness in rubber plantations compared with nearby forest habitat, with low beta diversity indicating spatial homogeneity of communities in rubber plantation. In addition, patterns of both functional alpha and beta diversities suggested the emergence of a functionally distinct ant community in the agroecosystem compared to the forest habitats. These results support a role of ecological filtering in structuring the taxonomic and functional composition of both habitats. This study highlights the need for a pluralistic approach to characterizing the loss of biodiversity in agroecosystems, as well as understanding the underlying mechanisms of community assembly driving this biodiversity loss.