Goat was an important source of milk and meat in addition to cow in dairy farming in Taiwan. Goat meat has becoming much more acceptable to consumers without regards of cultural and religious barriers. Therefore, selection of goats to improve growth traits was brought into action. Due to the poor growth rate and meat yield of Taiwan black goat (TB) breed in Taiwan, many exotic breeds were brought into breeding scheme to improve their growth trait. However, excessively crossbreeding alien species with TB decreased its population and their genetic variation, so which was considered as an endemic species in Taiwan that needed to be preserved. In recent years, the genetic markers were studied and applied in domestic animals, aiming at evaluating and selecting across breeds. Hence the objective of this study is using genetic marker to analyze genetic structure and its growth performance in Taiwan, setting the purpose of genetic improvement as well as to sustain the germplasm preservation. There were 15 sets of microsatellite markers used for analyzing 682 goats that sampled from 10 populations. The average number of alleles (Na) and effective alleles (Ne) were 11.87±3.4 and 5.1±1.8. The average expected heterozygosity (HE) and observed heterozygosity (HO) per locus were 0.781±0.081 and 0.602±0.116. Average polymorphic information content (PIC) was 0.747±0.103. FIS was 0.747. The results showed that 14 sets of microsatellite markers were highly polymorphic. The genetic distances between individuals were estimated using the method of Nei (1972) and followed by construction of phylogenetic tree using neighbor-joining (NJ) methods. The results indicated that these 15 sets of microsatellite markers were proved to successfully recognized different populations included. The germplasm of TB was still well-preserved in Hengchun Branch, LRI, C. O. A. Meanwhile, there were 3 single nucleotide polymorphism (SNP) markers being selected for analyzing their association with growth traits of Nubian goats in Taiwan. They were MSTN g.1256TTTTA/-, POU1F1 g.102T>G and IGFI g.282G>C according to their association with various productivity traits studied by several authors. In this trial, 497 Nubian goats were sampled. Growth traits data including body weight (BW), body length (BL), body height (BH), and body chest girth (BCG) at birth, weaning, 6-month-age, 9-month-age and yearling were collected. The average daily gain (ADG) at birth to weaning, weaning to 6-month-age, 6-month-age to 9-month-age and 9-month-age to yearling were also calculated, respectively. The association analysis revealed that 3 SNP markers had significantly effects. Individuals with BB genotype of MSTN gene showed better growth traits at BCG0, ADG6, BW6, and ADG9 among three genotypes (P < 0.05). Individuals with D1D1 genotype of POU1f1 gene showed better growth traits at BH6, BL6, BCG6, BW9, BH9, BL9, BCG9, BL12 and BCG12 among three genotypes (P < 0.05). Individuals with CC genotype of IGFI gene showed better growth traits at BW0, BL0, BCG0, BH6, BL6, BCG6, BL9, BCG9, BH12 and BL12 among three genotypes (P < 0.05). Overall, these 15 sets of microsatellite markers we used could apply for TB as well as hybrid goat population genetic structure for future conservation guidance, while growth traits association test also showed all three SNP markers have remarkable effects on it, provided practical application for meat goat breeding in Taiwan. As a result, marker-assisted selection (MAS) will promote rapid efficient breeding and selection of goat.