Sinocalycanthus chinensis, the only representative of the Sinocalycanthus genus belonging to the Calycanthaceae family, is an endangered shrub endemic to China. A combination of morphological traits and molecular markers may be the most reliable method to assess genetic variation among populations of this species. To provide crucial information for establishing strategies for the management and conservation of this species, the genetic variation among three populations of S. chinensis was assessed based on the morphological traits of fruits and seeds and on inter-simple sequence repeat (ISSR) profiles. We obtained the following results: fruit stalk length, fruit length, fruit weight, and seed number per fruit varied significantly among the three populations (P<0.05) with the highest values in the Damingshan(DMS) population, intermediate values in the Daleishan (DLS) population, and the lowest values in the Longxushan (LXS) population. Seed weight, seed length, seed width, and seed thickness were greatest in the DLS population, and were significantly higher than their respective values in the DMS and LXS populations (P<0.05). The phenotypic differentiation coefficient (V_ST) based on the morphological traits of fruits varied from 0.5518 to 0.9750, with a mean of 0.8930. All the variation existed among populations. The V_ST based on the morphological traits of fruits varied from 0.1669 to 0.8678, with a mean of 0.6240. Except for seed length, all the variation existed among populations. The percentage of polymorphic loci, Shannon informative index, and Nei's gene diversity were highest in the DMS population, intermediate in the LXS population, and lowest in the DLS population. The genetic differentiation coefficient (G_ST) among populations was 0.6050. The clustering results based on ISSR data showed that DMS and LXS populations were clustered into one group, and the DLS population joined to that group. The dendrogram was similar to that based on the morphological traits of seeds, but differed from that based on the morphological traits of fruits. There was a significant positive correlation between the mean variation coefficient of seeds and the genetic diversity indices, while there was no correlation between the mean variation coefficient of fruits and the genetic diversity indices. The V_ST based on the morphological traits of fruits was higher than the G_ST estimated from ISSR data, while the V_ST based on the morphological traits of seeds was similar to the G_ST estimated from ISSR data. This suggested that the morphological variations among seeds might be caused by genetic variations, while environmental factors might play important roles in forming the morphological variations among fruits. A Mantel test showed that there was no significant correlation between the genetic distance matrix based on the ISSR profile and the Euclidean distance matrix based on the morphological traits of fruits or seeds. This indicated that the variations among the morphological traits of fruits and seeds may be mainly affected by environmental factors, as well as genetic factors.