Punica granatum plants showing symptoms caused by root-knot nematodes were detected in the municipality of Majes, Arequipa, Peru. Based on the morphological, esterase phenotypes, and molecular analyses of the mitochondrial DNA region between the cytochome oxidase subunit II and 16 S rRNA genes (mtDNA) and species-specific sequence characterized amplified region, the causal agent of the observed symptoms was identified as Meloidogyne incognita. Pathogenicity was confirmed by fulfilling a modified version of Koch's postulates. To our knowledge, this is the first report of M. incognita infecting P. granatum in Peru.