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We determined the complete sequences of six size variants of intergenic spacer (IGS) region from one individual of the malaria vector mosquito species, Anopheles sinensis. All six size variants observed in this study show almost the same basic primary struc-ture in which three repeat regions (A, B, and C) are interspersed by highly conserved nonrepeating sec-tions. In contrast to the well-ordered subrepeating patterns found in A and C, the repeat region B dis-plays extremely variable and complicated profiles in the number and arrangement of subrepeat units among different size classes. It is apparent that the prominent level of length difference in the repeat regions B and C is responsible for the intragenomic length variations of the IGS molecule observed in the present study. High level of sequence homology and regularly arranged repeating pattern of 11 to 14 bp motif sequences har-bored within the B repeat region allow us to consider that these motif sequences may be associated with their potential role as a recombination site. Compared to those previously published in other mosquito spe-cies, the IGS of A. sinensis showed a very unique struc-tural format in subrepeat patterns of the IGS region. This result suggests that the structure and sequence profiles of the IGS region would provide useful infor-mation for the exploitation of a convenient molecular marker to identify morphologically complicated spe-cies complex and to characterize the genetic variation of population. This suggestion is far from being con-clusive at present, but a further genetic study will bring more compelling evidences for this pending issue.