The knowledge of the different population‐level processes operating within a species, and the genetic variability of the individual prokaryotic genomes, is key to understanding the adaptability of microbial populations. Here, we characterized the flexible genome of ammonia‐oxidizing archaeal (AOA) populations using a metagenomic recruitment approach and long‐read (PacBio HiFi) metagenomic sequencing. In the lower photic zone of the western Mediterranean Sea (75 m deep), the genomes Nitrosopelagicus brevis CN25 and Nitrosopumilus catalinensis SPOT1 had the highest recruitment values among available complete AOA genomes. They were used to analyse the diversity of flexible genes (variable from strain to strain) by examining the long‐reads located within the flexible genomic islands (fGIs) identified by their under‐recruitment. Both AOA genomes had a large fGI involved in the glycosylation of exposed structures, highly variable, and rich in glycosyltransferases. N. brevis had two fGIs related to the transport of phosphorus and ammonium respectively. N. catalinensis had fGIs involved in phosphorus transportation and metal uptake. A fGI5 previously reported as ‘unassigned function’ in N. brevis could be associated with defense. These findings demonstrate that the microdiversity of marine microbe populations, including AOA, can be effectively characterized using an approach that incorporates third‐generation sequencing metagenomics. This study utilized a metagenomic recruitment method and individual long‐read (PacBio HiFi) analysis to identify different versions of flexible genomic islands (fGIs) within a single population of two AOA species, Nitrosopelagicus brevis and Nitrosopumilus catalinensis, in the water column (lower photic zone) off the coast of the Western Mediterranean.