This study aimed to characterize two novelmcr-1variants,mcr-1.35andmcr-1.36, which originated fromMoraxellaspp. that were isolated from diseased pigs in China. TheMoraxellaspp. carrying novelmcr-1variants were subjected to whole-genome sequencing (WGS) and phylogenetic analysis based on the 16S rRNA gene. Themcr-1variantsmcr-1.35andmcr-1.36were characterized using phylogenetic analysis, a comparison of genetic environments, and protein structure prediction. The WGS indicated that two novelmcr-1variants were located in the chromosomes of threeMoraxellaspp. with a genetic environment ofmcr-1-pap2. In addition to the novel colistin resistance genesmcr-1.35andmcr-1.36, the threeMoraxellaspp. contained other antimicrobial resistance genes, includingaac(3)-IId,tet(O),sul2,floR, andblaROB-3. A functional cloning assay indicated that either themcr-1.35ormcr-1.36gene could confer resistance to colistin inEscherichia coliDH5α and JM109. The nucleotide sequences ofmcr-1.35andmcr-1.36presented 95.33 and 95.33% identities, respectively, tomcr-1.1. The phylogenetic analysis showed thatmcr-1.35andmcr-1.36were derived fromMoraxellaspp. that belonged to subclades that were different from those of themcr-1variants (mcr-1.1tomcr-1.34exceptmcr-1.10) originating from Enterobacteriaceae. The deduced amino acid sequences of MCR-1.35 (MCR-1.36) showed 96.67% (96.49%), 82.59% (82.04%), 84.07% (83.52%), 55.52% (55.17%), 59.75% (59.57%), and 61.88% (61.69%) identity to MCR-1.10, MCR-2.2, MCR-6.1, MCR-LIN, MCR-OSL, and MCR-POR, respectively, that originated fromMoraxellasp. Notably, protein structure alignment showed only a few changes in amino acid residues between MCR-1.1 and MCR-1.35, as well as between MCR-1.1 and MCR-1.36. In conclusion, this study identifiedMoraxellaspp. carrying two novelmcr-1variants,mcr-1.35andmcr-1.36, conferring resistance to colistin, which were isolated from pig farms in China. In addition,mcr-like variants were observed to be located in the chromosomes of some species ofMoraxellaisolated from pig samples.