To study the genetic polymorphisms of Y-chromosome-specific STR loci in Chinese of different surnames, 9 Y-STR loci were amplified by single fluorescent multiplex PCR and the PCR products were detected by using ABI PrismTM 3100 DNA Sequencer. Samples were randomly-selected from male blood donors in ShenZhen. These individuals, who were otherwise unrelated, had the most common surnames among Chinese as their surnames, namely Li, Wang or Zhang. There were 139 subjects with surname Li, 118 with surname Wang and 119 with the surname Zhang. In the Li population, a total of 126 haplotypes was found and 118 of them were unique, with a haplotype diversity 0.9974. In the Wang population, a total of 105 haplotypes was found and 94 of them were unique, with a haplotype diversity of 0.9953. In the Zhang population, a total of 101 haplotypes was found and 88 of them were unique, with a haplotype diversity of 0.9964. Our results indicated that the genetic polymorphisms of Y-STR haplotypes at these 9 loci in unrelated male individuals with Chinese surnames of Li, Wang or Zhang are highly polymorphic and showed no significant differences with our previous data of haplotype polymorphisms in unrelated male individuals from the Chinese ethnic Han population.