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Introduction. The bla CTX-M-3 gene has rarely been reported in Morganella morganii strains and its genetic environment has not yet been investigated. Aim. To identify the bla CTX-M-3 gene in M. morganii isolated from swine and characterize its genetic environment. Methodology. A M. morganii isolate (named MM1L5) from a deceased swine was identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and subjected to antimicrobial susceptibility testing. The bla genes were detected and then the genetic location and environment of bla CTX-M-3 were investigated by Southern blot and PCR mapping, respectively. The M. morganii bla CTX-M-3 gene was cloned and expressed in Escherichia coli . Results. Isolate MM1L5 harboured the bla CTX-M-3 and bla TEM-1 genes. The bla CTX-M-3 gene, located on the chromosome, was co-carried with an IS 26 and bla TEM-1 gene by a novel 6361 bp IS 26 -flanked composite transposon, designated Tn 6741 . This transposon consisted of a novel bla CTX-M-3 -containing module, IS 26 -ΔIS Ecp1-bla CTX-M-3 -Δ orf477 -IS 26 (named Tn 6710 ), and a bla TEM-1 -containing module, IS 26 -Δ orf477-bla TEM-1 -tnpR-IS 26 , differing from previous reports. Phylogenetic analysis showed a significant variation based on the sequence of Tn 6741 , as compared to those of other related transposons. Interestingly, although the cloned bla CTX-M-3 gene could confer resistance to ceftiofur, cefquinome, ceftriaxone and cefotaxime, one amino acid substitution (Ile-142-Thr) resulted in a significant reduction of resistance to these antimicrobials. Conclusion. This is the first time that bla CTX-M-3 has been identified on a chromosome from a M. morganii isolate. Furthermore, the bla CTX-M-3 gene was located with an IS 26 element and bla TEM-1 gene on a novel IS 26 -flanked composite transposon, Tn 6741 , suggesting that Tn 6741 might act as a reservoir for the bla CTX-M-3 and bla TEM-1 genes and may become an important vehicle for their dissemination among M. morganii .