Shellfish allergy is a major global health concern, with prawns being among the most common elicitors of allergic reactions. This project describes a comparative allergenomic analysis of the most widely consumed prawn species worldwide: black tiger prawn (Penaeus monodon) and white leg prawn (Litopenaeus vannamei). The aim of the study was to comprehensively characterize and compare their allergen profiles, with a particular focus on relative allergen abundance and species-specific expression patterns. Raw protein extracts from P. monodon and L. vannamei were analyzed using label-free shotgun proteomics by LC–MS/MS. Protein identification and quantification were performed using standard database searching workflows. Allergen candidates were predicted in silico using AllerCatPro 2.0, and crustacean allergens with strong evidence were selected for downstream analysis. Relative allergen abundance was assessed using intensity-based absolute quantification (iBAQ%), while differential expression between species was evaluated using label-free quantification (LFQ) intensities. Although allergens constituted a small proportion of the identified proteome, they accounted for a substantial fraction of total protein abundance in both species. Major known prawn allergens, including myosin light chain, arginine kinase, sarcoplasmic calcium-binding protein, and tropomyosin, were detected in both species, alongside several low-abundance proteins identified as potential novel allergen candidates. Species-specific differences in allergen expression were observed at the level of allergen orthologs, isoforms, and variants, with subsets of allergens uniquely detected in each species. This dataset provides a resource for studying species-specific variation in prawn allergen composition and abundance and supports future work on shellfish development and standardisation of allergy diagnostics, therapeutic strategies, and risk assessment.