The ninja element, originally isolated from an unstable white mutant strain white-milky (w^mky) of Drosophila simulans, is a member of the retrotransposon family with long terminal repeats (LTRs). We show that ninja is present in high copy numbers in the w^mky-derivative sublines white-chocolate (w^cho) and white-persimmon1 (w^psm1), in a low copy number in another derivative subline white-milky 3 (w^mky3), and in only a few copies in a wild type strain. We have cloned the ninja elements from these sublines and examined their structures. Most of the elements cloned (38 out of 41 independent clones) from w^cho were full length. In contrast, only 9 of 23 independent clones from w^mky3 were full length. We hypothesize that ninja elements were integrated and lost frequently in the w^mky strain and its derivative genomes, and that a rapid decrease in numbers of the ninja element was caused not by an increased rate of loss but by a reduction of integration of full length ninja elements in w^mky3. Each defective element had a unique deletion and/or an insertion except for the three from w^mky3, which had exactly the same 81-bp deletion in each of the 5 and 3 LTRs. The 5 and 3 ends of the deletion appeared to represent sequences similar to those of Drosophila consensus splicing sites. Ectopic splicing may have produced these defective ninja elements.