28Resistance to insecticides has evolved in multiple insect species, leading to increased application 29 rates and even control failures. Understanding the genetic basis of insecticide resistance is 30 fundamental for mitigating its impact on crop production and disease control. We performed a 31 GWAS approach with the Drosophila Genetic Reference Panel (DGRP) to identify the mutations 32 involved in resistance to two widely used classes of insecticides: organophosphates (OPs, 33 parathion) and pyrethroids (deltamethrin). Most variation in parathion resistance was associated 34 with mutations in the target gene Ace, while most variation in deltamethrin resistance was 35 associated with mutations in Cyp6a23, a gene encoding a detoxification enzyme never previously 36 associated with resistance. A "nested GWAS" further revealed the contribution of other loci: 37Dscam1 and trpl were implicated in resistance to parathion, but only in lines lacking Wolbachia. 38Cyp6a17, the paralogous gene of Cyp6a23, and CG7627, an ATP-binding cassette transporter, 39 were implicated in deltamethrin resistance. We observed signatures of recent selective sweeps at 40 all of these resistance loci and confirmed that the soft sweep at Ace is indeed driven by the 41 identified resistance mutations. Analysis of allele frequencies in additional population samples 42 revealed that most resistance mutations are segregating across the globe, but that frequencies can 43 vary substantially among populations. Altogether, our data reveal that the widely used OP and 44 pyrethroid insecticides imposed a strong selection pressure on natural insect populations. 45