The origins of Kam-Sui speaking Chadong and Mulam people have been controversial subjects in ethnic history studies and other related fields. Here, we studied Y chromosome (40 informative single nucleotide polymorphisms and 17 short tandem repeats in a non-recombining region) and mtDNA (hypervariable segment I and coding region single nucleotide polymorphisms) diversities in 50 Chadong and 93 Mulam individuals. The Y chromosome and mtDNA haplogroup components and network analyses indicated that both Chadong and Mulam originated from the admixture between surrounding populations and the indigenous Kam-Sui populations. The newly found Chadong is more closely related to Mulam than to Maonan, especially in the maternal lineages.