Population structure concerning P element activity was investigated in two natural Drosophila populations. These populations are very different as far as in the viability spectrum is concerned. In one population, the Raleigh, United States population, genetic loads related to viability have been kept at a fairly high level. In the other population, the Nagasaki, Japan, population, the genetic loads tend to be stable at very low levels. In the Raleigh population it is estimated that on the average 4 copies of intact P elements that possess transposase activity exist in the genome. On the other hand only 0.7 complete copies are estimated to exist in the genome of the Nagasaki population. Heterogeneity in the P element copy number and significant positive linkage disequilibrium among occupied sites were detected in the Raleigh population. Our results, with some evidences which indicate that high mutation rate was caused by the P element, suggests that the large genetic loads in the Raleigh population are caused by the rapid invasion of P element in this population.