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Mitochondrial cytochrome b (Cytb) and partial control region (CR) DNA sequence of 165 individuals out of eight pig breeds (Laiwu Black, Dapulian Black, Licha Black, Yimeng Black, Yantai Black, Wulian Black, Luyan White and Changwei White) from Shandong province of China were sequenced to determine phylogenetic relationships and to what extent they were affected by modern commercial breeds (Landrace, Yorkshire and Duroc) in maternal lineage. The eight breeds from Shandong had lower maternal evolutionary divergence than the three commercial breeds. Additionally, they shared the same haplotype (T2) of Cytb. All these results suggest they may have originated from closely related maternal ancestors, if not from a single ancestor. The fact that haplotypes of Dapulian Black and Laiwu Black formed their own subclades, while those of other breeds of Shandong dispersed in the Asian clade of the tree based on CR, indicates that Dapulian Black and Laiwu Black are indigenous breeds with relatively independent maternal lineage, while the others have extensively gene flow with other breeds. Except in Luyan White, no European haplotypes were found in pig breeds from Shandong, demonstrating the maternal introgression from the modern commercial pigs has had no or very little impact on the breeds from Shandong. Comparatively, CR is more suitable to analyze the phylogenetic relationships of closely related groups, whereas the four SNPs of Cytb are useful to determine whether modern commercial breeds (Duroc, Landrace and sometimes Yorkshire) were used as dam in the breeding process of new breeds or synthetic lines in China. [ABSTRACT FROM AUTHOR]