The objective of this study was to evaluate the physiological quality of pepper seeds as a function of maturity, presence of seeds in fruits and storage. Pepper seeds used for the study were collected in July 2009, from plants grown in greenhouse belonging to Embrapa Roraima sector of technology transfer. The experimental design was entirely randomized under a (3 x 2 x 2) factorial scheme. At harvest, immature, intermediate and ripe fruits were collected, totalizing 90 fruits. Extraction of seeds was immediate in part of fruits, and therest of fruits were left for 10 days at room temperature at 25 °C. Seed physiological quality was evaluated concerning germination, germination speed. The tests were repeated three months after harvest to assess storage aspects. According to results, the maturation stages that showed better physiological quality were the seeds originated from green orange color fruits (intermediate class) as compared to those obtained from ripe (intense red color) fruits and immature (green) fruits. Seed permanence within fruits for ten days improved its physiological quality among early harvested fruits (intermediate). Seeds extracted from fruits ten days after harvest showed better physiological at three months of storage, when compared to seeds extracted immediately after harvest.