Jackfruit (Artocarpus heterophyllus L.) is native to South and Southeast Asia, one of the largest and most nutritionally dense tropical fruit crops in the world. Generally, jackfruit can be categorized into hard or soft flesh types based on its fruit texture, but several other fruit textures are also mentioned in the local market. The objective of this study is to identify favorable fruit morphometric traits that may be co-inherited with diverse fruit textures. To do this, we categorized 73 accessions of jackfruit genotypes into four major fruit types named “Khaja”, “Gala”, “Rosha”, and “Improved Gala” based on 18 fruit morphometric traits. Meanwhile, genetic diversity was assessed using 8 iPBS (inter-primer binding site) retrotransposon markers for a total of 13 selected accessions from different fruit types. We observed significant pomological variation (coefficient of variation (CV%), 0–109) within and among different fruit types, three of which are important for tree selection, which are organoleptic test (0–12), fruit weight (2–12.5 kg), and total suspended solid value (2–22 TSS). UPGMA (unweighted pair group method with arithmetic mean)-based cluster analysis of traits, clustered the accessions in four major clusters, representing high diversity among the accessions. Moreover, the first three components of principal component analysis (PCA) explained only 55% of the variation suggests that fruit type alone does not sufficiently explain the multifactorial pattern observed in the dataset. Overall, the Improved Gala type showed the best eating quality (as determined by organoleptic tests) and the highest total soluble solids (TSS, sweetness), while Khaja had the highest fruit and bulb sizes. We found that the accessions had moderate genetic diversity (0.13) with Shannon's index (0.6). Bayesian-based STRUCTURE analysis exhibits a total of seven clusters, where sub-grouping or admixture among them was noticeable. Moreover, clusters generated from pomological and iPBS markers showed a clear discrepancy, most probably due to nonlinear trait marker association and the effect of environmental variation on pomological traits. Our results have the potential to become useful for future research focused on jackfruit tree selection, improvement, cultivation, and orchard management.