Objective To study the genetic polymorphism of Nanjiang yellow goat and to investigate the feasibility of this research by AFLP. Methods The genomic DNAs of 15 goats were analyzed with RAPD and AFLP molecule marking techniques. The effects of the two methods were compared. Results The rates of the polymorphic loci and the genetic similar index of population by RAPD marker were 26.98% and 0.942 respectively, and that by 31.4% AFLP and 0.874 respectively. Conclusion AFLP and RAPD technique are effective methods in genetic polymorphism monitoring of Nanjiang yellow goats, and supply useful parameter with appraise genetic stability.