The Pacific oyster, Crassostrea gigas, is an economically important mollusk species cultured throughout the world. This species has a haploid complement of 10 metacentric chromosomes. Chromosomal identification is essential in genomic research. The most frequently used technique for molecular cytogenetics studies is fluorescent in situ hybridization (FISH) which offers new opportunities for the identification of oyster chromosomes. The Pacific oyster BAC (Bacterial Artificial Chromosome) library contains 73,728 C. gigas clones with an average insert size of 152 kb representing a 11.8-fold genome coverage. Some of these clones were tested for chromosomal identification in C. gigas. A few clones were mapped by BAC-FISH on C. gigas chromosomes. The BAC clones studied are chromosome-specific and allowed the identification of several chromosome pairs of C. gigas. Some of these clones are already sequenced, so we could assign some genes and sequences to specific C. gigas chromosomes. This preliminary BAC-FISH physical map of C. gigas will provide a foundation for comparative genomics and chromosome evolution in oysters.