Since its initial discovery in an Escherichia coli isolate from China, mcr-1 has been detected in Escherichia coli, Klebsiella pneumoniae and Salmonella enterica, and is rarely reported in other Enterobacteriaceae. Here, we report the isolation and identification of a Shigella flexneri strain harboring mcr-1 from stool samples in a pig farm in China from 2009.