While shellfish species are widely consumed due to their nutritional advantages, they are also among the top eight food items for food-borne allergies. Five distinct thermal processing techniques were applied to the crustacean to investigate the tropomyosin level variations caused by heat processing. Fresh shrimp and prawns were utilized as controls for the determination of allergen-encoding genes. Prior to molecular analysis, the proximate composition and acidity of raw and processed samples were also performed. The yield and purity of DNA were also determined. Melting curve and gel electrophoresis tests verified the existence of allergen-coding genes. Thermal processing procedures affected the proximate composition, particularly the total protein and fat concentrations, according to the findings. Following the heat treatment, the pH levels decreased, particularly in the grilled samples. There were also significant differences in the quantity and quality of the extracted DNA. Regardless of crustacean species, the tropomyosin-encoding gene was detected in both fried and grilled samples. These findings demonstrated that RT-PCR identification and validation of the crustacean allergy gene by gel electrophoresis might be a reliable approach for the thermally treated shrimp and prawn samples. This study shows that investigating the allergen coding gene might provide a viable way for detecting food-borne allergens in other thermally processed food items, which are becoming more concerned about food safety.