Mustard (Brassica spp.) stands as India's second largest oilseed crop while mustard aphid infestations from Lipaphis erysimi Kalt. result in substantial crop yield losses. The sustainable approach to controlling pests involves the development of plants that are insect-resistant. Mustard secondary metabolites such as glucosinolates, phenols and sugars determine how aphids establish themselves and grow. The research team chose ten genotypes which included five resistant and five susceptible genotypes based on their Mean Aphid Index Value (MAIV) and Mean Aphid Multiplication Index Value (MAMIV). The research team conducted biochemical analyses on seeds, inflorescences, leaves and stems. RP-9 (73.91 μ mole/g dry wt.) seeds contained the most glucosinolate content among genotypes. The study found that MAMIV showed a strong negative correlation with higher glucosinolate content which resulted in lower aphid reproduction. RP-9 (3.04 mg/g dry sample) leaves contained the highest phenol content while MAIV and MAMIV displayed strong negative correlations with phenol levels in seeds and inflorescences. Sugar content was highest in RH-406 (17.95mg/g dry sample) seeds, which displayed a highly significant negative correlation with MAIV. The results demonstrate that plants develop resistance through specific tissue distribution of glucosinolates, phenols and sugars. This research suggests that these compounds can function as biochemical markers that breeders can use to create mustard genotypes that possess sustainable resistance against L. erysimi.