The genome of Drosophila melanogaster strain y cn bw sp has been sequenced and the transposable elements insertion sites have been determined. We hybridized fluorescence-labeled probes directed to the hobo transposon, Dm412 and mdg1 retrotransposons to polytene chromosomes and compared the observed sites to those published in the annotated genome sequence. We observed an almost twofold increase in the number of hobo hybridization sites (46 found as compared to 24 annotated sites). There was no evidence that the hobo transposition rate is slowing over the 10-year period. The patterns of Dm412 and mdg1 sites have changed less dramatically since the time of genome sequencing. Three novel Dm412 hybridization sites were detected while 4 out of 30 annotated sites were missing. Only one additional mdg1 site was found, while 1 out of 29 annotated sites has been lost.