We perform inversion of seismic waveforms for three-dimensional (3-D) models of shear and compressional seismic wave velocities (VS and VP, respectively) in the lowermost 400 km of the mantle (the D″ region) beneath Central America and the Caribbean. We use data primarily from USArray stations. Our models reveal vertically continuous high-velocity anomalies from 400 km to 0 km above the core-mantle boundary (CMB). Most areas between two vertically continuous high-velocity anomalies immediately above the CMB show low-velocity anomalies, while the areas beneath Colombia from 300 km to 100 km above the CMB show low-VS and high-VP anomalies. The regions with positive correlations between VS and VP anomalies are interpreted as primarily thermal heterogeneities. Thus, the high-velocity anomalies throughout the D″ region are interpreted as the subducted paleo-Farallon slabs, and the low-velocity areas between slabs suggest the presence of a passive plume. The regions where VS and VP are negatively correlated suggest the presence of chemical heterogeneities. One of the most likely candidates is the phase transition of SiO2 from CaCl2-type to α-PbO2-type included in portions of the D″ region where material with mid-ocean ridge basalt (MORB) composition is concentrated. MORB supplied by the subducted Farallon paleo-slab could accumulate in the D″ region, leading to self-heating and partial melt generation.