Passion fruit (Passiflora spp.), an underutilized and unexplored fruit crop, holds significant potential for improving nutritional health in tropical and subtropical regions. This study aimed to characterize various genotypes of passion fruit including yellow (G1, G3, G5), purple (G2, G4, G10), sweet (G6, G7, G9) and giant (G8), collected from different regions in Tamil Nadu, India, based on morphological, yield and biochemical traits. A comprehensive evaluation of morphological, yield and quality traits, combined with advanced statistical analysis, including correlation studies and principal component analysis (PCA), identified genotypes with desirable traits, offering valuable resources for breeding programs to improve passion fruit cultivation. The analysis included biometric data, yield performance and quality traits, complemented by molecular diversity assessment using ISSR markers. Significant variation was observed across morphological and biochemical traits; genotype G8 showed the highest fruit weight and juice content, while genotype G7 had the highest total soluble solids and sugar content. Principal component analysis (PCA) and hierarchical clustering revealed distinct groupings, providing insights into their genetic diversity and potential for future crop improvement. These findings suggest that specific genotypes could be strategically targeted for breeding programs to enhance yield, fruit quality and resilience in passion fruit cultivation.