Pigeon racing appeals to many in Taiwan, due in part to the potential large financial gains based on illegal betting. The races are unregulated with frequent examples of fraud, such as substitution of one bird for a substandard one. There is no test available to reliably verify the bloodline of pigeons and thus help to resolve such disputes. In this study, we describe a multiplex PCR amplification system combining 7 STR loci and a chromo-helicase DNA binding gene (CHD) marker for the identification of individual pigeons. The cumulative power of discrimination (CPd) of the 7 STR loci was 0.99999234 based upon our population study. The cumulative probability of paternity (CPP) when used in paternity testing of 17, and the combined probability of exclusion pigeon families ranged from 97.36 to 99.99% (CPE) was 0.9325 for these seven STR markers. The statistical data illustrates the potential of this system to be used in pigeon individualization and paternity testing. Furthermore, the established STR system could be also used in the other areas, such as ecology, population genetics, and avian breeding programs.