High throughput sequencing was used to assess the soil prokaryote (16S rRNA) and fungal (ITS rRNA) communities of five vegetation types (evergreen broad-leaved forest, deciduous broad-leaved forest, mixed coniferous-broad-leaved forest, coniferous forest , and secondary shrub for four seasons in a secondary subtropical forest in Eastern China. The goal was to determine the relative importance of vegetation type and season on the soil microbial community.