The influence of seasonal variation on the bacterial and archaeal diversity of the mangrove soil in Sitio Sabang, Barangay Cabayugan, Puerto Princesa, Palawan, Philippines was investigated. Sample collections were done in three selected sampling sites along the Sabang River during the dry and wet seasons of 2017. The prokaryotic community structures were determined by Next-Generation Sequencing (NGS) targeting the V3–V4 regions of the 16S rRNA gene, using Illumina Hiseq 2500. Results showed that the soil microbial community in the Sabang mangroves was predominantly inhabited by members of the Phyla Proteobacteria, followed by those of Phyla Chloroflexi and Bacteroidetes. Members of Phyla Firmicutes, Bathyarchaeota, Actinobacteria, Acidobacteria, Euryarchaeota, Cyanobacteria and the DHVEG-6 cluster were also present in varying relative abundance. There was no significant difference in the prokaryotic community structures between the dry and wet seasons, which implies that mangrove health and its microbial resources have been conserved. Significant differences were observed only for the relative abundance of Proteobacteria and Firmicutes (more abundant in wet season), and Acidobacteria, Chloroflexi and DHVEG-6 cluster (more abundant in dry season). The steep species diversity curves indicate that several other microbial species are yet to be discovered. Additional sampling and further molecular surveys of the Sabang mangrove prokaryotic community structure for at least 2 yr are thus recommended.