The genetic diversity of 10 Pinus tabulaeformis natural secondary forest populations in northern China and the correlation with environmental factors were analyzed by using ISSR molecular marker techniques. 250 individuals were amplified 137 bands by using 13 ISSR primers. The average percentage of polymorphic loci is 60.72%, and there is significant difference between different populations with the highest value in BTM group (71.53%) and the lowest value in YLG group (51.09%). Expected heterozygosity index and Shannon's information index(I) individually range from 0.2824-0.3702 and 0.1923-0.2490 respectively between different geographic populations, and their average values are 0.3210 and 0.2165 respectively. The genetic variety between different populations are 37.53% of total genetic diversity. Among 10 P. tabulaeformis natural populations, genetic distances range from 0.083 (LKS to CJC) to 0.2939 (SDC to DWP), geographic distances range form 110.9252 km (LKS to SDC) to 1741.0933 km (YWL to YLG). Genetic distance and geographic distance are uncorrelated in the Mantel test (r=0.069, P=0.360). UPGMA clustering analysis showed that YWL, LKS, CJC, YLGY and SDC populations were a group, and MS population was clearly separated from other populations, and the other four populations were clustered into a group. The populations located in the boundary of the second and the third topography steps of China (YWL、BTM、YLGY) have a high level of genetic diversity, and the populations in critical distribution areas have a low level. The correlation analysis of genetic diversity and environmental factors showed that allele number and polymorphic percentage of natural populations were a significant positive correlation with the annual average temperature, the average temperature in January, the extreme minimum temperature, and were significant negative correlation with altitude. With increasing annual maximum temperature and the altitude, decreasing in annual rainfall, Shannon's information index rises. Finally, get a result that the molecular variation of P. tabulaeformis natural secondary forest population have partly geographical variation.