Formosan wild boar (Sus scrofa taivanus) is the endemic subspecies in Taiwan and it played a crucial cultural role in aborigines. These days, the molecular biology technologies helped us to deeply realize the value of animal conservation in National Park by combining the studies of molecular biology, traditional biology, and anthropology. The Formosan wild boar samples obtained in Nantou Danda region nearby National Park were analyzed. Then, the phylogenetic relationship tree was constructed by the mitochondrial D-loop regions and indicated a unique clade, 34 Formosan wild boar individuals of 41 samples which divided into 14 haplotypes clustered in this clade. In the other hand, the remained 7 individuals possessed the mitochondrial DNA sequences of Lanyu pigs revealed part of Formosan wild boars already had gene introgression from Lanyu pigs. Comparing the mitochondrial D-loop sequences of wild boars from Asian continent and neat islands, Formosan wild boar possesses genetic closer lineage to Fujian wild boar than Ryukyu wild boar. By 19 microsatellite markers, the mean allelic numbers in 26 individuals were 7.58, and the effect numbers of allele were 4.09. The polymorphism index content (PIC) value was 0.683, indicated that the selected microsatellite markers were polymorphic enough and it fitted the analysis of population genetic in Formosan wild boars. FIS value was 0.2778, it imply the mean heterozygosity lower. We investigated the hunting status in the neighbor areas of Yu-shan National Park. Hunting dogs are specialized to trace wild boars, and increase the hunting stress in the population of wild boars by them. For convenient administration, wild boars rear pens near houses or farms. The major source of wild boars was catched from the forests. Some of wild boars crossbred with domesticated pigs for increasing their offsprings’ performance by feeders. It should pay a attention to the consequence of cross-breeding leads the domestic individuals gene introgress into the wild boar individuals located in National Park.