Purpose <p>The multidrug-resistant fungal pathogen <i>Candida auris</i> poses an increasing global health threat due to its high transmissibility and persistence in healthcare environments. We aimed to explore the potential cases of mixed <i>C. auris</i>-strain colonizations or infections in China and to investigate the genetic and biological diversity of the associated isolates.</p> Methods <p><i>C. auris</i> isolates from 5 colonization or infection cases were distinguished by colony morphology and verified by D1/D2-ITS alignment. Phylogenetic and genomic diversity analysis of all isolates were conducted using whole genome sequences. Comparative biological analysis of all isolates, including cellular and colony morphology, antifungal susceptibility, biofilm formation, SAP activity, and both in vitro and in vivo survival capabilities were performed.</p> Results <p>Five cases of potential mixed <i>C. auris</i>-strain colonization or infections in China were identified. Comparative genomic analysis revealed these cases involved strains from two distinct genetic clades (I and III) or strains from the same clade but with genetic alterations. Comparative biological analysis demonstrated the strains from mixed colonization or infections exhibit differences in several key aspects, including colony morphology, biofilm formation, SAP activity, and both in vitro and in vivo survival capabilities.</p> Conclusion <p>Comparative analyses revealed notable differences in biofilm formation, environmental survival, and secretion of virulence factors between the co-colonizing or co-infecting strains of <i>C. auris</i>. These biological and genetic disparities may present significant challenges for the diagnosis and treatment of <i>C. auris</i> infections, as strains with different genetic backgrounds may exhibit varying abilities to colonize host or environmental niches.</p>