Fermented fish waste – Gunapaselam (FFW-G) is rich in nutrients which can be exploited for agronomic purpose. Vigna radiata used in crop rotation increases the fertility of soil by biological nitrogen fixation. But currently the yield of Vigna radiata is reduced due to various factors including unsustainable application of chemical fertilizers that made the soil barren. Leaves play an important role in the overall performance of the plants. The present study analysed the effect of organic fertilizer, fermented fish waste – Gunapaselam on photosynthetic pigment level, total soluble sugar, nitrate, protein, mineral content and anatomical changes in the leaves of Vigna radiata. Experimental field study group includes Group I- Water; Group II – Chemical fertilizer (25:50:25:20 kg NPKS ha-1) and Group III- 1:100 diluted FFW-G. Fertilization with FFW-G has induced anatomical changes in the leaves of Vigna radiata which would increase the biosynthetic capacity. Application of FFW-G increased the photosynthetic pigment level which results in an increase in the amount of total sugars, nitrate, protein and mineral content (NPK) in the leaves of Vigna radiata. The results clearly confirm that application of FFW-G improves the biochemical components and structural features of Vigna radiata leaves. Thus, this kind of organic fertilizer will improve the photosynthetic efficiency of Vigna radiata and hence the yield.