The main aim of this research is to study the degradation of the seed storage protein in different varieties of lentils (Lens culinaris) during germination which involve different interval time. Brown lentils and black lentils were selected for this experiment. Seeds were germinated for 24,48,72,96, and 120 hours in the dark condition. Total crude protein was calculated by Kjedahl method and water soluble and water insoluble protein also was calculated for germinated seeds. Changes in weight of black lentils and brown lentils was recorded where the weight of both lentils increased with the time of germination due to higher moisture content. Water soluble proteins also kept on decrease rapidly in both lentils during different germination. Total crude protein present in black lentil was about 37% and 33 % for brown lentils. Water soluble protein is high at 0 hour for black lentils which was 17% and 16% for brown lentils. Degradation of seed storage proteins profiles was further analyzed with sodium dodecyl sulphate polyaccrylamide gel electrophoresis (SDS-PAGE). The degradation of protein decreased from high molecular polypeptide (HMW) due to germination process which activates metabolic enzyme activity. Legumin and vicilin was identified in the protein fraction of lentils. In conclusion, SDS—PAGE of germinated seed storage can be considered as economical way to assess genetic variation and also can be used as markers for further identification.