IntroductionPomegranate (Punica granatum L.) peels are rich in various bioactive compounds. Characterization of these compounds is crucial for the utilization of peel waste in industrial processing.ObjectiveThe study aimed (1) to establish and compare the metabolic profiles of the peel of seven pomegranate cultivars and (2) to identify bioactive compounds contributing to the larvicidal activity against the third instar larvae of Culex pipiens.Materials and MethodsUPLC‐ESI‐MS/MS was utilized to analyze peel methanol extracts of different pomegranate cultivars. The larvicidal activity was determined by calculating the larval mortality among the third instar larvae of C. pipiens. Multivariate data analysis was conducted to identify the metabolites that exhibited a larvicidal effect.ResultsA total of 24 metabolites, including hydrolyzable tannins, flavonoids, and alkaloids, were tentatively identified in both negative and positive ionization modes. The extract of cultivar ‘Black’ exhibited the most potent larvicidal effect with LC50 values of 185.15, 156.84, and 138.12 ppm/mL after 24, 48, and 72 h of treatment, respectively. By applying chemometric techniques, the larvicidal activity could be directly correlated to the bioactive compounds punicalagin, quercetin‐O‐rhamnoside, quercetin‐O‐pentoside, and galloyl‐HHDP‐glucose.ConclusionThe present study implemented UPLC‐ESI‐MS/MS and chemometric techniques as potential tools for metabolomics analysis and differentiation between peels of different pomegranate cultivars. In addition, cultivar ‘Black’ extract could be a promising natural insecticide against mosquitoes since it is rich in bioactive compounds with larvicidal activity.