Crocosphaera watsonii (UCYN-B), a unicellular nitrogen-fixing cyanobacterium in oligotrophic oceans, plays an important role in Marine nitrogen and carbon cycling. Due to its narrow ecological niche, Its ecology and evolutionary pattern has remained unknown. Here, we explored population-level genetic diversity of natural UCYN-B population spatially through metagenomics analysis. Our results showed that the UCYN-B population in the northwest Pacific Ocean had a higher intra-population genetic diversity (i.e., micro-diversity), which was 2.5 times larger than the public data on average. The decay rate of linkage disequilibrium and the four-gamete test showed that homologous recombination was common, and the higher the temperature, the higher homologous recombination rate (p=0.034), To assess the impact of selection, the number of non-synonymous sites/synonymous sites(pN/pS) indicated that all UCYN-B population was under a positive selection(pN/pS>1), and a lower surface iron concentration leaded to a higher number of nonsynonymous sites (p=0.038). meanwhile, the ratio between the linkage disequilibrium measured by r² on N and S polymorphisms (r²N/r²S) indicated that UCYN-B population was driven by temperature(p=0.0091) and surface iron concentration (p=0.016). In terms of the gene function, UCYN-B population was limited not only by iron and phosphorus but also by photosynthesis and nitrogen in some sites (pN/pS values were higher than those of the other functions). In summary, our results indicated the drivers of natural populations of UCYN-B, while we also confirmed that diazotroph was constrained beyond iron and phosphorus  limitations in their natural environment.