Flowering period and longevity play important roles in determining the quality of commercial flowers. Marker-trait associations for eight flowering and 12 ornamental traits have been studied using a GLM and MLM analysis with a set of 2099 AFLP polymorphic markers in Chrysanthemum. The GLM model identified 453 markers for phenotypic traits whereas the MLM association analysis model revealed a total of 197 significant marker-trait associations for the phenotypic traits. The strongest association was detected between AFLP markers with a bud diameter trait, which explained 68% of the variation. Among several polymorphic bands, 14 markers were associated with senescence, 10 with flower diameter and eight with stem length. This approach also led to the identification of seven markers with significant association to full bloom. Therefore, these markers can be used for the genetic improvement of the ornamental value of Chrysanthemum after further confirmation. The analysis of the results revealed a number of markers co-associated with different correlated phenotypic traits. The results revealed informative markers that have shown a significant correlation with several traits which could be useful for breeding programs and other analyses associated to future studies of Chrysanthemum.