Lycopene is the pigment principally responsible for the characteristic deep red color of ripe tomato fruits and its content varies considerably during post-harvest ripening. It, as a natural source of antioxidants, has attracted attentions due to its biological and physicochemical properties. In this study, lycopene content was observed at different post-harvest stages of green house grown and field grown tomatoes. Tomato was harvested at breaker stage; and it was treated as 0 Days. The lycopene was estimated at the interval of 0, 15 and 30 days post-harvest. The lycopene count in mg/100 g was measured in a spectrophotometer at 503 nm. It was observed that lycopene increased in successive post-harvest stages. For QTLs identification, single marker analysis was performed and observed that Two SSR markers Leaat003, TOM184, were associated with fruit lycopene content.