A total of 16 fungi were isolated from seeds of 29 flax cultivars. The isolated fungi were Alternaria alternata, Stemphylium botryosum, Aspergillus flavus, A. niger, Chaetomium sp., Cladosporium sp., Drechslera sp., Epicoccum sp., Fusarium solani, F. oxysporum, Nigrospora sp., Penicillium sp., Phoma sp., Stemphylium sp., Trichoderma sp., and Verticillium sp. A. alternata, S. botryosum, A. flavus, Cladosporium sp., and Penicillium sp. were the only fungi, which were isolated from all the tested cultivars. Associations among the pairs of isolated fungi were identified and the relative strength of their associations were measured by calculating Pearson correlation coefficient (r) for each pair of the fungi. From 45 to 91 fungal pairings were analyzed each year. Thirty six of the fungal pairs were significantly associated. Of the 36 pairs, 32 were positively associated, and 4 were negatively associated. No significant associations were found in the remainder fungal pairs. Grouping the isolated fungi by cluster analysis, based on their seed colonization patterns, was not related to their taxonomy. Cluster analysis divided the fungi into two distinct groups. One group was consisting of 10 fungi, and a second group was consisting of 6 fungi. Within each group, the fungi were associated strongly and positively, whereas between groups, the fungi were associated weakly or negatively. This result implies the potential existence of cultivar related groups of fungi.