Abstract: In this paper,the sequence features of the introns associated with lowly expressed genes and highly expressed genes of Drosophila embryo were studied.The results show that the characteristics of these two kinds of gene introns are significantly different from each other.The average length of the first introns in highly expressed genes is 2.62 times than that in lowly expressed genes.And the average length of the second introns in highly expressed genes is 1.79 times than that in lowly expressed genes.It is found that the CpG islands contents in first introns of two types of genes are higher compared to other introns.Moreover,the CpG islands content in introns of highly expressed genes is higher than lowly expressed genes.In addition,the frequencies of TATA box,CAAT box and GC box occurred in introns of highly expressed genes is significantly higher than those of lowly expressed genes too,especially in first introns.We also extracted 6-mer Simple Sequence Repeat (SSRs) which occurred frequently in the first introns of two different expression genes.Some of these SSRs are accordance with potential transcription factor binding sites (TFBS),which are verified by experimental analyses.These results provide theoretical evidences for that the introns,especially the first introns,may play an important role in the transcriptional regulation and thus influence the level of expression of Drosophila embryo genes.