Two inversions in the opposite arms of the third chromosome are common in natural populations of Drosophila ananassae. When the strains are taken to laboratory, these inversions have been found to persist for several generations. Four natural populations were sampled and the data on the combinations between 3L and 3R karyotypes were obtained. For all the four populations, laboratory stocks (mass culture and isofemale lines) were established and maintained in food bottles by transferring fifty flies in each generation. After ten generations, chromosomes of all stocks were sampled. The results show that the two linked inversions are associated randomly in natural populations and in laboratory stocks established from mass culture. On the other hand, the same two inversions show non-random association (linkage disequilibrium) in several isofemale lines. The random association between inversions in natural and mass culture laboratory populations as contrasted to laboratory populations established from single females suggest that random drift is the cause of non-random association in isofemale lines. The tight linkage between the two inversions as evidenced by the results of recombination studies reported earlier, supports the notion that linkage disequilibrium is caused by drift.