The government of China defined 56 official ethnicities for the ethnic groups in China for political purposes; however, there are many more than 56 ethnic groups. Therefore, similar groups must be pooled for registry, and the so-called ethnicity identification is an important official mission in China. Here, we showed how genetics can help in the ethnicity identification for the Gelong people on Hainan Island. The Gelong speak a Kadai language whose other speakers (officially of the Gelao ethnicity) are all far in the southwest of China. Being registered as a Han ethnicity, the Gelong lost all the benefits assigned to the minorities. Y-chromosome typing was performed in a sample of 78 individuals. Twenty single nucleotide polymorphisms (SNPs) and seven short tandem repeats (STRs) were typed and eight haplogroups were detected, among which haplogroup O1a* was the most dominant. Compared with the Y haplogroups of the populations in south China, the Gelong were found to be closest to the Gelao and the Hlai using principal components (PCs) analysis, dendrogram clustering and STR networks. The genetic similarity between the Gelong and the Hlai may have resulted from the gene flow during thousands of years of neighboring history on Hainan Island, whereas the similarity between the Gelong and the Gelao may have resulted from their common ancestry because there is less possibility of gene flow over such a far distance. As both linguistic and genetic evidence support the similarity between the Gelong and the Gelao, we suggest that the Gelong register as Gelao for their official ethnicity. However, this identification is invalid until it is accepted by the Gelong people themselves and the Hainan government.