In order to assessing the resistance to Fusarium oxysporum f.sp. Lentis in different genotypes of lentil and its relation to protein markers, a research was programmed using 38 genotypes of lentil in Greenhouse and laboratory conditions. Analysis of studied traits was performed as a factorial experiment with two levels for Factor A (conditions without disease and conditions for disease) and 38 levels (genotypes) for Factor B based on completely randomized design with three replications. Our data showed that the average mortality of plants in the eighth week was more than the fourth week dpi. The mean comparison of studied traits by using LSD test (p=0.01) indicated that they are in different demographic groups. According to the results of cluster analysis, genotypes were divided into three groups, which were differed in the average mortality rate. Analysis of water and salt-soluble proteins showed that the average genetic variation for all loci is 0.5 and the average of Shannon index is 0.34. In the SDS-PAGE analysis for seed storage protein, genotypes were divided into three groups in cluster analysis. Regression analysis of data from proteins and water-soluble salt with morphological traits showed that regression coefficient for the average mortality of plants in the fourth and eighth week with marker 12 was significant (p=0.01). Markers 4 and 12 because of having ties with more than one trait were identified as the most effective markers. It seems that in breeding programs for resistance to the disease, protein markers can be utilized in addition to morphological traits.