ABSTRACT UCYN‐A is a phenomenal diazotrophic cyanobacterium with significant ecological importance. UCYN‐A1 and UCYN‐A2 are the two most abundant ecotypes. Recently, the striking discovery of nitroplast, a novel N 2 ‐fixing organelle in cultured B. bigelowii /UCYN‐A2 endosymbiont, indicated the possibility that UCYN‐A2 has evolved beyond endosymbiosis to an early phase of organellogenesis. This study addresses the following critical question: What evolutionary heterogeneity has emerged between UCYN‐A1 and UCYN‐A2? To investigate this issue, we comprehensively compared a total of seven genomes from UCYN‐A2 and UCYN‐A1. Under similar genome organizations, GC content, and gene composition, we still detected abundant genetic differences, including group–unique orthogroups, ANI below 85%, and 577 UCYN‐A2‐unique INDELs in single‐copy orthologous genes (SCOGs). Moreover, we also focused on the orthologous genes of 40 metabolic‐pathway genes in nitroplast. In addition to high‐informative SNPs and INDELs possessing distinct interlineage differences, we traced abundant codon usage “signatures” that serve as lineage‐unique molecular markers. Most notably, we successfully established a strain‐level identification map for UCYN‐A strains using codon aversion motifs, which represents the first case study of this approach in bacteria. In summary, all the comparative results reported here collectively indicate that UCYN‐A1 and UCYN‐A2 have evolved remarkable genomic heterogeneities. Furthermore, the findings of this work will definitely promote our current understanding of codon aversion and the evolution of UCYN‐A.