Abstract: Bael identified as endangered medicinal tree is propagated through seeds. Use of quality seed enhance the seedling quality characters and is highly valid in developing nursery management techniques. In perennial crops, quality seeds are obtained by proper selection of fruits. Tree crops produce fruits with physical polymorphism due to developmental and environmental variation. Hence studies were formulated to evaluate the influence of fruit polymorphism on seed quality characters. Fresh bael fruits were collected from five different locations of Coimbatore. The fruits were categorized based on the width into three different groups as large (10-12 cm), medium (8-10 cm) and small (6-8 cm). The large and medium fruits recovered to 32 and 39%, respectively from bulk. Then seeds were extracted and evaluated for seed quality characters along with seeds of bulk fruits. The physiological quality characters measured in germination room revealed that seed germination observed with seeds of large fruits were higher (82%) and were followed by seeds of medium (74%), bulk (68%) and small (60%) fruits. The seedling vigour measured through root (12.5 cm) and shoot length (13.9 cm), drymatter production (613 mg) and vigour index (2164) also exposed the superiority of seeds of large fruits. The measurement of biochemical characters as oil content was more with seeds of medium fruits (42.8%) than other size distributions, while the differences were non significant for seed protein and electrical conductivity. The seeds sown in polybag nursery also expressed that seeds of large fruits produced vigourous seedlings.