<p>Bael (<i>Aegle marmelos</i> (L.) Correa) is a magnificent but underrated fruit species with medicinal and religious value. This study used 36 morphological, yield, and fruit quality variables to investigate the genetic diversity of 21 bael cultivars in rainfed, hot, semi-arid climates, including a local genotype and a national check (NB-5). Important characteristics such fruit color, shape, size, locule arrangement, thorn, seed, and fiber quality were found to exhibit morphometric variability. Principal component analysis (PCA) revealed that the first eight components described 87.50% of the overall variation, with the first component alone explaining 32.42%. Fruit weight and pulp weight were strongly and positively correlated with total and non-reducing sugars (r = + 1.0). Hierarchical clustering grouped the cultivars into three distinct clusters, Cluster I (varieties 1, 3, 5, 6, 7, and 9) exhibited higher means for fruit width, girth, weight, shell weight, and shell thickness, making them suitable candidates for yield-based selection. Cluster III cultivars demonstrated superior qualitative traits, including elevated levels of ascorbic acid, non-reducing sugar, total sugar, antioxidants, total phenolics, total flavonoids, and total soluble solids. These results are useful for selecting and breeding bael varieties with improved quality and production traits, as well as creating functional foods and nutraceuticals made from bael because of its therapeutic qualities. Future studies may concentrate on using the best cultivars found to extract and market bioactive substances that may have therapeutic uses. Lastly, the great genetic diversity of bael cultivars highlights their potential for both economic exploitation and genetic improvement, especially in dry and semi-arid environments.</p>