The use of biopharmaceutical products that comprise therapeutic antibodies are increasing in the pharmaceutical industry. Chinese hamster ovary (CHO) cell lines are widely used in the field of pharmaceutical industry to produce therapeutic antibodies. CHO DG44 cell line is a dihydrofolate reductase (DHFR)-deficient line, which is frequently used as a host cell while applying the gene amplification method. Since the chromosomes of CHO cells are unstable, variation in chromosome number occurs in these cells. This study focused on the dynamics of each chromosome during changes in the number of chromosomes. Clones from the CHO genomic bacterial artificial chromosome (BAC) library, a powerful tool that is expected to cover the entire CHO DG44 genome , were used to distinguish the location of individual chromosomes. In addition to the BAC clones previously known to correspond to the chromosomal locations of CHO DG44 and CHO K1 cell lines , sequences of 304 BAC clones that can identify the chromosomal locations in CHO DG44 cell line have been determined in this study. Therefore, our study leads to an understanding of the DNA sequence of individual chromosomes in the genome and the stability of each chromosome to establish high-producing CHO cell line.