To investigate the genetic basis of cross-resistance to insecticides, we conducted genetic analyses of resistance to three organophosphate insecticides, malathion, prothiophos, and fenitrothion. After isofemale lines resistant and susceptible to all of the three organophosphates had been screened from natural populations of Drosophila melanogaster (Meigen), chromosomal analyses were performed by using chromosome-substituted lines between the resistant and the susceptible lines. The chromosomal analyses revealed that both the second and the third chromosomes contributed to resistance to the organophosphates, suggesting that this resistant line possessed at least two factors for organophosphate resistance. However, the relative contribution of each chromosome was different in resistance to different organophosphates. We further carried out genetic mapping of a resistance factor for each organophosphate on each of the two chromosomes. Each resistance factor was mapped to the position of each chromosome, about II-62 and III-50. Results of the chromosomal analyses and the genetic mapping revealed that at least two resistance factors exhibiting different patterns of cross-resistance to the organophosphates existed within a natural population of D. melanogaster. Based on this research, genetic variation in insecticide resistance within natural populations and complex as well as simple aspects of the mechanism of cross-resistance are discussed.