There has been an increasing focus on traditional crops for food security. ‘Bhat’ is an indigenous soybean variety from the Indian Himalayan Region that is available in diverse seed color, shapes, and sizes. The crop is valued as a traditional food and medicine but has been ignored due to changing food habits. A study was conducted to establish nutritional diversity and genetic relatedness in ‘bhat’ genotype indigenous to the Garhwal division of Uttarakhand in the Western IHR. 52 soybean accessions were collected from different villages and analyzed for macro and microelements using HHXRF (Hand Held X-ray Fluorescence) spectroscopic technique and Atomic Absorption Spectroscopy (AAS), and protein content (by Kjeldahl method). The results showed ‘bhat’ to be an extremely nutrient-rich crop that can benefit hill populations. The samples were found to have high levels of calcium (highest concentration 27300 ppm), followed by phosphorus, potassium, and sulphur. Among the micronutrients, silicon was the most dominant (highest concentration 1920 ppm), followed by iron, zinc, and manganese. The samples also had high amounts of proteins (as high as 43.56%). 25 polymorphic simple sequence repeats (SSR) markers were employed to ascertain genetic diversity. Only 13 molecular markers showed amplification and based on phylogenetic analysis the genotypes were grouped into 4 major clusters having visually distinct phenotypes in each group, indicating the mixing of population and loss of authenticity. The study highlights the need for concerted efforts towards sustainable utilization of this nutrient-rich crop, and designing of ‘bhat’ specific molecular markers for crop identification.