<p>Citrus seeds are rich in protein, oil, carbohydrates, and bioactive compounds and contain significantly less water than peel and pulp, rendering them prime candidates for value-added product development. This study focused on characterizing the phytochemical composition of the seeds from four huanglongbing-tolerant citrus genotypes (HLB-TCG). Due to their value in biomedical applications, limonoids, flavonoids, coumarins, phenolic acids, amino acids and stilbenoids were measured in HLB-TCG seeds using LC–MS/MS. The HLB-TCG seeds were particularly rich in limonoids, and had high concentrations of individual flavonoids, such as naringin, narirutin, and hesperidin. The ‘Sunki’ seeds were rich in polymethoxylated flavones, especially tangeretin and nobiletin. Furthermore, all common amino acids were present, with phenylalanine, arginine, and asparagine being particularly abundant. Additionally, based on the ratio of total polyunsaturated fatty acids (FA) to total saturated and monounsaturated FA, as well as cloud point, pour point, and viscosity index, we conclude that there is potential for utilizing these seeds for biodiesel production. Moreover, higher concentrations of natural antioxidants like phytosterols and tocopherols suggest better performance of biodiesel due to protection against oxidation. Together, this data suggests the potential utilization of HLB-TCG seeds for value-added applications, such as isolation of bioactive compounds and biodiesel production.</p>