Matrix association region (MAR) is not only a kind of cis-acting element for regulation of eukaryotic gene expression and chromosome dynamics, but also a type of fixed and specific DNA marker on the eukaryotic chromosomes. MAR library can be constructed by in vitro or in vivo association of DNA fragments with the nuclear matrix. In vitro MARs can be used in construction of chromosome's physical map, and in vivo MARs can be applied in studying the expression, regulation and chromosomal organization of known genes, and analyzing the newly discovered genes.