DNA sequence analysis of the same chromosomal region from two haplotypes of Mus musculus and from the related species M. caroli and M. pahari reveals the presence of long interspersed sequence one (LINES-1, or L1) elements residing at the same nucleotide position in the two most distantly related of the species (M. musculus and M. pahari). The DNA sequence of each of these L1 elements is more similar to that of other L1 elements from its own species than to the other. Thus, the L1 sequence at each of these sites is recent with respect to the divergence of the species. This could be a result of recent gene conversion of L1 elements inherited from a common ancestor or of two recent independent L1 insertion events at the same nucleotide position in the two species. Such specificity of insertion would be quite different from the apparent randomness of other characterized L1 insertion events, such as those in the beta-globin locus. If the recent L1 sequences arose at this site by gene conversion of an ancestral L1 element, then the absence of an L1 element at this location in the M. caroli chromosome examined could arise either from its precise deletion from M. caroli or from the segregation into M. caroli of a polymorphic chromosome present in the ancestral population which was missing this L1 element.