In linseed, marker-trait associations were studied for 15 morphological and nutraceutical traits using a 50microsatellite markers with a set of 170 elite genotypes. Using regression based association analysis, each of the 15 traitswere regressed on 111 available polymorphic alleles. A total of 21 SSR markers gave significant associations with at leastone of the traits. The number of markers associated with individual traits ranged from 1 to 4. Plant height showed significantregression with only one SSR marker, while 1000 seed weight and seed yield per plant showed significant regression on4 SSR markers. SSR markers Lu144a-1, Lu151-2 and Lu138-4 were associated with number of capsules per plant at1% significance level. Similarly three SSR markers viz. Lua49B (allele number one), Lua60 (allele number one) and Lua125a(allele number three) were significantly associated alpha linolenic acid content at 0.1% significance level (P£0.001). FourSSR markers namely Lu151-2, Lua68-2, Lu138-3 and Lu143-1 were associated with 1000 seed weight. SSR markersLu236-2, Lu144a-1, Lu151-2, and Lu143-2 were significantly (P£0.001) associated with seed yield per plant. Lub14-4 andLu143-1 were associated with oil content in seeds. Association explained 7 to 44.2 per cent of the variation of individualtraits. Markers identified by this study will be useful for marker-assisted breeding after necessary validation.