Determination of association between molecular markers and agronomic traits provides an excellent tool for marker-assisted selection. In this study, multivariate stepwise regression analysis was used to estimate associations between SSR markers and some agronomic traits in saffron ecotypes. Two-year average values for the measured traits were used for association analyses. The results of stepwise regression analysis revealed significant associations between the traits and some of the studied loci. More than one informative marker was detected for most of the traits. Totally 25 informative SSR markers were identified in two years. Markers SCA382, SCA15 and SCD219 were associated with most traits under both years. These markers are considered to be relatively more reliable. Among the SSR primers, special attention should be drawn to primers SCA382, SCA15, and SCD219, which had the highest associated fragments with most traits in two years and could be considered for use as candidate markers in marker-assisted selection.