In this study, the genetic diversity and association ananlysis of 128 Dendrobium germplasms were conducted using 29 phenotypic traits and 15 SSR markers. The results showed that the coefficient of variation of 29 phenotypic traits ranged from 12.26% to 145.64%, and the diversity index ranged from 0.08 to 1.50. The highest and lowest coefficients of variation were observed for inflorescence length and leaf variegation, respectively. Quantitative traits of the floral organs exhibited highly significant positive intercorrelations. Cluster analysis divided the 128 Dendrobium germplasms into five groups. Analysis using the 15 SSR primers identified 98 alleles, with mean values of 3.742 for effective alleles (Ne), 0.345 for observed heterozygosity (Ho), 0.618 for expected heterozygosity (He), 1.320 for Shannon's index (I), and 0.631 for polymorphism information content (PIC). Based on population structure analysis and principal coordinate analysis (PCoA), the 128 germplasms were grouped into two subpopulations. A total of 8 markers were significantly associated with thirteen phenotypic traits according to the general linear model (GLM) and mixed linear model (MLM) models, explaining 8.68% to 22.30% of phenotypic variation. This study provides feasible markers for molecular marker-assisted selection of important ornamental traits in Dendrobium germplasms, which will enhance the breeding efficiency of this species.