Citrus is one of the most significant fruit crops in the Rutaceae family. The Northeastern Himalayan region of India and the foothills of the Central and Western Himalayan regions, often referred to as the “treasure house of citrus germplasm” are rich sources of citrus genetic diversity. The present study aimed to assess the morphological and biochemical variabilities among different mandarin (Citrus reticulata Blanco) germplasms cultivated/grown in Eastern India. Following ICAR-National Bureau of Plant Genetic Resources (NBPGR) descriptors, a comprehensive survey and exploratory collection were conducted from native populations across West Bengal, Sikkim and Nagaland during 2024–25, covering diverse altitudinal and agro-climatic conditions. Mandarins collected from Dzongu (North Sikkim) exhibited the highest fruit weight (112.98 g) and total soluble solids (TSS: 10.13 ± 1.08 °Brix), along with superior vitamin C content (33.48 ± 4.44 mg/100 mL) and TSS:Acid ratio (20.87 ± 3.97), suggesting superior sweetness and nutritional quality. In contrast, Tseminyü (Nagaland) recorded the lowest fruit weight (61.05 g) and highest titratable acidity (1.04 ± 0.08 %), while Rüsoma (Nagaland) showed the highest reducing sugar (4.67 ± 1.98 %) and large fruit size (fruit length 57.62 mm, width 63.38 mm). Overall, the study revealed considerable genetic variability among the collected accessions, identifying Dzongu and Rüsoma as promising sources for quality planting material and breeding programs aimed at fruit quality improvement in mandarin. High-quality planting material can be produced using the accession.