Variation of microbial species diversity has typically been explained as the outcomes of local ecological factors driving species coexistence, overlooking the roles of evolutionary constraints. Here, we argue that macro-evolutionary phylogenetic niche conservatism and unequal diversification rates among phylum-level lineages are strong determinants of diversity–environment relationships in bacterial systems. That is, apart from stochasticity, environmental effects operate most strongly on phylum composition, which in turn dictates species diversity of bacterial communities. This concept is demonstrated using bacterioplankton in surface seawaters of the East China Sea. Furthermore, we show that the species richness of a local bacterioplankton community can generally be estimated based on relative dominances of phyla and their contributions of species numbers in the global seawater pool — highlighting an important influence of evolutionary constraints on local community diversity.