BackgroundThe strand-biased circularizing integrative elements (SEs) are putatively non-mobilizable integrative elements for transmitting antimicrobial resistance genes. The transposition mode and the prevalence of SEs in prokaryotes remain vague.ResultsTo corroborate the transposition mode and the prevalence of SEs, hypothetical transposition intermediates of an SE were searched for in genomic DNA fractions of an SE host. Then, the SE core genes were defined based on gene knockout experiments, and the synteny blocks of their distant homologs were searched for in the RefSeq complete genome sequence database using PSI-BLAST. A genomic DNA fractionation experiment revealed that SE copies are present in a double-stranded nicked circular form in vivo. Operonic structure of three conserved coding sequences (intA,tfp, intB) andsraplocated at the left end of SEs were identified as essential forattL×attRrecombination. The synteny blocks oftfpandsraphomologs were detected in 3.6% of the replicons ofGammaproteobacteriabut not in other taxa, implying that SE movement is host-dependent. SEs have been discovered most frequently in the ordersVibrionales(19% of replicons),Pseudomonadales(18%),Alteromonadales(17%), andAeromonadales(12%).Genomic comparisons revealed 35 new SE members with identifiable termini. SEs are present at 1 to 2 copies per replicon and have a median length of 15.7 kb. Three newly identified SE members carry antimicrobial resistance genes, liketmexCD-toprJ,mcr-9, andblaGMA-1.Further experiments validated that three new SE members possess the strand-biasedattL×attRrecombination activity.ConclusionsThis study suggested that transposition intermediates of SEs are double-stranded circular DNA. The main hosts of SEs are a subset of free-livingGammaproteobacteria; this represents a rather narrow host range compared to those of mobile DNA element groups discovered to date. As the host range, genetic organization, and movements are unique among the mobile DNA elements, SEs provide a new model system for host-mobile DNA element coevolution studies.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13100-023-00295-5.