Citrus indica and C. macroptera are the wild endangered species of Citrus occurring in northeastern India. Surveys were undertaken in this region for ascertaining distribution, studying variability and for collection of germplasm of these two species. C. indica, an endemic species of this region, was collected from the Citrus Gene Sanctuary located in buffer zone of Nokrek Biosphere Reserve in the Garo hills of Meghalaya. In addition, a putative natural hybrid of C. indica and C. limon was collected for the first time from the south Garo hills. C. macroptera had much wider distribution and was collected from Mizoram and Meghalaya states. In Jantia hills of Meghalaya, natural populations of this species are in a highly threatened state. The two species were unevenly distributed all over the explored territory. Morphological characterization of leaves, fruits and seeds indicated the presence of sizable variability within collected accessions of these two Citrus species. Indigenous technical knowledge gathered on the use and socio-economic importance indicated commercial potential for these two species in northeastern India. However, lack of cultivation of these species and clearing of forest cover at an alarming rate has led to an urgent need to adopt complementary conservation strategies to safeguard these species and to ensure their availability for future utilization. A major emphasis on developing methods for their propagation, multiplication and regeneration in in situ and ex situ conditions is required.