Abstract: SRAP markers were conducted to scan the whole genome of 180 samples of Pinus yunnanensis with different stem forms from 6 populations. Furthermore, the different unique bands produced by different stem forms samples were cloned and sequenced for comparison, so as to predict the candidate genes for regulating stem forms variation. The results showed that 584 bands were amplified by selected 14 primer pairs of SRAP, of which 551 bands were polymorphic, with a percentage of 94.35%. An average of 41.7 bands and 39.4 polymorphic bands was amplified by per primer pair, respectively. The number of effective alleles (N_e) and Nei's gene diversity (H) among 6 populations was ranged from 1.4516 to 1.4872 and from 0.2703 to 0.2904, and N_e value was 1.3655–1.4541 and H value was 0.2181–0.2687 among stem forms in 6 populations, respectively. Meanwhile, genetic differentiation coefficient (G_st) and gene flow (N_m) among 6 populations was 0.1573 and 2.6787, and G_st was 0.0087 and N_m was 56.7002 among stem forms in 6 populations, respectively. These indexes indicated that there was frequent gene flow and low genetic differentiation among different populations and different stem forms of P. yunnanensis. The sequences analysis of 26 unique different bands between straight and twist stem forms indicated that catalase (kat A gene), endonuclease, glycosyl hydrolase and AN1 zinc finger protein (SAP6) may be involved in the regulation of the stem form development of P. yunnanensis.