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The larvae of C. capitata occupy a discontinuous environment constituted by rotting fruits of several plant species. The consequences of this condition on the genetic structure were studied in a natural population by analyzing the polymorphism at the Est-1 (pupal esterase) locus by means of Wright's fixation indices. The results indicate that each fruit is colonized by a finite and small number of inseminated females (about four). The relations among the corresponding FIS, FITand FSTindices of each one of the three alleles detected in the population was not the same and the genotypic frequencies in the whole population differed from Hardy–Weinberg expectations, suggesting that some kind of selection might be acting on the Est-1 locus or linked loci.