Abstract: To reveal the variation characteristics and genetic basis of cones of different parents of Cunninghamia lanceolata, and explore the molecular markers associated with cone morphology, morphological characteristics of the C. lanceolata cones in Guangdong third-generation seed orchard that harbors 50 parents were investigated. On the basis of analysis of genetic diversity, the study made association analysis of the cone morphological data with SRAP markers. The results showed that the morphological characteristics of cones were significantly different among the parents. Phenotypic variation coefficients of each traits ranged from 11.01% to 31.90%, and the genetic variation coefficients spanned from 8.13% to 21.54%. The repeatability of all traits was consistently higher than 0.8, indicating that cone traits were controlled by strong genetic factors. Moreover, there were 59 markers were significantly associated with 8 traits. Among them, the 9, 10, 6, 3, 6, 9, 8 and 8 markers were significantly associated with cone vertical diameter, cone horizontal diameter, single cone fresh weight, cone volume, number of bract scale layers, total number of bract scale, bract scale length, bract scale width, respectively.