The male-specific lethal (MSL) complex, which includes two noncoding RNA on X (roX)1 and roX2 RNAs, induces histone H4-Lys16 acetylation for twofold hypertranscription of the male X chromosome in Drosophila melanogaster. To characterize the role of roX RNAs in this process, we have identified evolutionarily conserved functional domains of roX RNAs in several Drosophila species (eight for roX1 and nine for roX2). Despite low homology between them, male-specific expression and X chromosome-specific binding are conserved. Within roX RNAs of all Drosophila species, we found conserved primary sequences, such as GUUNUACG, in the 3' end of both roX1 (three repeats) and roX2 (two repeats). A predicted stem-loop structure of roX2 RNA contains this sequence in the 3' stem region. Six tandem repeats of this stem-loop region (72 nt) of roX2 were enough for targeting the MSL complex and inducing H4-Lys16 acetylation on the X chromosome without other parts of roX2 RNA, suggesting that roX RNAs might play important roles in regulating enzymatic activity of the MSL complex.