Abstract: Based on the statistical comparative analysis,some potential transcriptional regulatory motifs in the sequences from upstream promoter to the end of the first intron of the ribosomal protein(RP)genes of fruit fly were extracted.About 85% of these motifs were accordant with the binding sites of sometranscriptional factors.After pairing the above motifs and comparing to a set of background sequences,we detected some motif pairs with statistical significance both in occurrent numbers and distance distributions in the RPgenes of fruit fly by using Hypergeometric distribution and Kolmogorov-Smirnov test respectively.These motif pairs were considered as potential synergistic motifs.The synergy of some of these motif pairs had been verified by biological experiments.Checking the positions of these motif pairs in the promoter sequences,we found that their main synergistic regions were in the upstream regions,whilethe synergy between upstream regions and introns was also an important form of combined regulation.For the majority of the motif pairs,we also found that the distance between two motifs was less than 300bp.Meanwhile,the combined motif pairs between upstream regions and other regions were closeto the first exon.These results would be helpful in understanding the mechanisms of thetranscriptional regulation for RPgenes in fruit fly.