To investigate genetic characteristics of the native cattle in Southeast Asian countries, we genotyped seven genes associated with economical traits, coat color, and hereditary disorder including SCD, SREBP1, EDG1, DGAT1, NCAPG, MC1R, and F11 genes in populations of Laotian native cattle by PCR or PCR-RFLP. The genotyping results indicate that only one genotype were observed in EDG1, DGAT1, NCAPG and F11 genes, suggesting that these genes are fixed to one allele in the populations of Laotian native cattle. On the other hand, two and three genotypes were observed in SCD and SREBP1 genes and the frequencies of the minor alleles of these genes were 0.09 and 0.20, respectively. For MC1R gene, two genotypes E+E+ and E+e were observed and frequencies of ED, E+, and e alleles were 0, 0.94, and 0.06, respectively. Our findings of the presence of these polymorphisms in zebu cattle are of particular interest regarding the origin of these polymorphisms. The sequence analysis of the D-loop region of mitochondrial DNA indicated that the Laotian native cattle possess three haplotypes that classified into a group of the zebu cattle haplotypes. The present findings will be informative for understanding the genetic characteristics of the native cattle of Southeast Asian countries.