We present new starch grain and phytolith data from two sites in Puerto Rico: Maisabel and HU-7. Our findings reveal a strong emphasis on the use of maize, followed by chile pepper and arrowroot in Early and Late Ceramic Age deposits. Manioc was rare, with nearly all manioc residues coming from Early Ceramic Age artifacts in the Maisabel site. Integrating both starches and phytoliths provides a more accurate view of plant use than if only one or the other of these classes of microfossils are studied. We then review previously reported microbotanical findings from the island to document the diversity of plant resources utilized by precolonial occupants of Puerto Rico and how commonly these resources occur. There is now a sufficient body of residue data available to allow new insights into precolonial agricultural economies of Puerto Rico. Applying ecological measures of diversity, richness, and evenness to microbotanical datasets for Puerto Rico reveal declines in diversity for both the initial and later colonizing populations of the island. These findings are consistent with expectations from agroecology, whereby productive domesticates are identified and over time exploited in greater proportions to other taxa, both wild and domesticated.