The non-LTR retrotransposons forming Drosophila telomeres constitute a robust mechanism for telomere maintenance, one which has persisted since before separation of the extant Drosophila species. These elements in D. melanogaster differ from nontelomeric retrotransposons in ways that give insight into general telomere biology. Here, we analyze telomere-specific retrotransposons from D. virilis, separated from D. melanogaster by 40 to 60 million years, to evaluate the evolutionary divergence of their telomeric traits. The telomeric retrotransposon HeT-A from D. melanogaster has an unusual promoter near its 3′ terminus that drives not the element in which it resides, but the adjacent downstream element in a head-to-tail array. An obvious benefit of this promoter is that it adds nonessential sequence to the 5′ end of each transcript, which is reverse transcribed and added to the chromosome. Because the 5′ end of each newly transposed element forms the end of the chromosome until another element transposes onto it, this nonessential sequence can buffer erosion of sequence essential for HeT-A. Surprisingly, we have now found that HeT-A in D. virilis has a promoter typical of non-LTR retrotransposons. This promoter adds no buffering sequence; nevertheless, the complete 5′ end of the element persists in telomere arrays, necessitating a more precise processing of the extreme end of the telomere in D. virilis.telomeres | retrotransposons | end replication problem | promoter evolution H eT-A, TART, and TAHRE are non-LTR retrotransposons that maintain the telomeres in Drosophila melanogaster. They transpose only to chromosome ends, where they form long arrays of head-to-tail repeats that make up the telomeres. Despite their differences, this retrotransposon mechanism for extending chromosome ends is functionally equivalent to the telomerase mechanism. In each case, an RNA template is reverse transcribed to add DNA repeats to the chromosome. Telomerase repeats are short sequences copied from part of the enzyme's RNA component. In Drosophila, each repeat is a copy of one of the three telomerespecific retrotransposons. These retrotransposons have unusual features, some in common, some not, but all presumably related to their role at the telomere (reviewed in refs. 1, 2). This study of species differences in the HeT-A promoters lends insight into the mechanisms by which HeT-A elements protect chromosome ends.A notable feature of D. melanogaster HeT-A is its promoter, which has unexpected similarities to promoters of retroviruses and LTR retrotransposons (3). HeT-A promoter sequences are found at the 3′ end of each element, in the 3′untranslated region (UTR). They direct transcription of the neighbor immediately downstream, rather than the element in which they reside (see Fig. 1). To an outside observer, if the downstream element is another HeT-A, the combined sequence (consisting of the 3′ sequence of the upstream element plus the entire downstream element) appears to be, and is formally equivalent to, an LTR retrotransposon ...