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Nodule bacteria (rhizobia) forming nitrogen-fixing symbiosis with legumes have a multicomponent genome represented by chromosome and a number of plasmids of different sizes. Genes related to symbiotic activity of Sinorhizobium meliloti are located predominantly on two megaplasmids SMa and SMb (1.35 and 1.68 Mb, correspondingly). Genomes at about 80% of native rhizobia nodulating alfalfa contained cryptic plasmids with sizes varied from 7 up to 450 kb. Functional role of this class of plasmids remained unclear up to the postgenomic era. Using two high-throughput sequencing methods (MiSeq and nanopore), the complete genome sequences of three S. meliloti strains native to the Aral Sea area were done in this work. Two cryptic plasmids of the strains AK23 and AK89, and two cryptic plasmids of the strain AK555 were assembled and annotated by using bioinformatics approaches (Flye, Racon, Medaka, Pilon, Prokka). Whole genome sequence data for the strains AK21 and AK83 harboring per two cryptic plasmids are from GenBank. The objective of the study was a joint comparative analysis of the 8 cryptic plasmids of the 5 native strains of S. meliloti from one population adapted to saline environment. The average size of three and two plasmids was at about 225 and 400 kb, correspondingly, while sizes of other three plasmids was greatly different (from 31 kb up to 152 kb). Plasmids of similar size (209 kb) showed 99% identity in genetically distinct strains, besides that replicon of SMd (31 kb) of the AK555 showed 86% homology to half-replicon of pSINME02 of the AK83. All plasmids were screened for replication systems and repABC locus was detected in cases of the 6 plasmids, while some of these and other two plasmids contained additional locus, or single repA, repB or repC genes. No correlation between sizes and replication systems was detected for tested plasmids. The sequences of all plasmids were analyzed for ORFs and their affiliation with COGs groups. The number of ORFs on tested plasmid replicons was ranged from 34 up to 506, while in each particular case all detected ORFs were belonged to the next four functional groups: i) cellular processes and signaling, ii) information storage and processing, iii) metabolism and iv) poorly characterized. Proteins homologous to type IV restriction endonucleases responsible for protection of bacteria cells from invading foreign DNA, like phages, were identified on 209 kb plasmids. These proteins are relating to bacterial immune systems. Summarizing, cryptic plasmids of native S. meliloti strains adapted to salinized environment are varied greatly in sizes, replication systems and harbored ORFs relating to vitality and immune system of bacteria. Obtained data strongly evident that non-symbiotic plasmids of S. meliloti involving in horizontal gene transfer harbored ORFs essential for environmental fitness of rhizobia. [ABSTRACT FROM AUTHOR]