Microbial communities are a key functional factor in soil that influences agricultural activities. Bacterial communities are responsible for nutrient transformation for the benefit of plant health and productivity. Despite this importance, most of the soil microbial diversity remains uncultured and knowledge of their structure generally demands robust molecular-based analysis. The goal of the current project was to estimate the diversity, relative abundance, and composition of the microbial communities associated to three Caribbean soils through a pyrosequencing-based analysis. Pyrosequencing (bTEFAP) of the V2-V3 region of the 16S rRNA gene was employed to assess the bacterial composition from the soil samples. Rarefaction curves, Shannon and Chao indexes were calculated by using MOTHUR and the data base SILVA. From a total of 55,438 sequences obtained in all soil samples processed, 31,348 were assigned to a particular order. An average of readings recovered from each soil sample was 10,334 and operational taxonomic units (OTUs) numbers did not exceeded 1,197. For all soil samples studied the majority of sequences (72%) were affiliated with unclassified microbes and the remaining (28%) to the domain Bacteria. Within Bacteria, the phylum Proteobacteria represented about 20% of each soil sample, while Alphaproteobacteria was the dominant class, except in the soil collected from the municipality “Maria La Baja”, where Betaproteobacteria was the predominant class. Actinobacteria was the second more dominant taxonomic group in all soil samples studied independent of origin, followed by Acidobacteruas and Bacteroidetes. The soil sample that showed the vast diversity at the phylum level was the municipality of “Maria La Baja”. The distribution of some bacterial phylogenetic groups and subgroups in the Caribbean soils studied correlated with soil properties such as pH, organic carbon content, total nitrogen and phosphorous content as well as to the presence and abundance of three functional and cultured soil microbial subgroups: Actinomycetes, Non-Sulfur Photosynthetic Bacteria (NSPB) and Lactic Acid Bacteria (LAB).