As climate change induces habitat shifts, bioclimatic variables are used in suitable habitat modeling to predict species migration. Begonia aborensis Dunn of sect. Sphenanthera (Hassk.) Warb. (Begoniaceae), a native species to Abor hills was categorized as 'Rare' in India. The study aimed to generate ecological niche modeling of B. aborensis, identify the influential bioclimatic factors, and trait analysis to detect the informative morphological traits of the species by ancestral reconstruction. Maxent version 3.3.3 was employed for ENM at 30 arc-second which showed an AUC value < 1, and highly suitable habitats in parts of Arunachal Pradesh, Meghalaya, and Nagaland. The annual precipitation, precipitation of the driest month, elevation, and annual mean temperature were found as the most influential bioclimatic predictors. The Representative Concentration Pathway (RCP) scenarios of greenhouse gas emission for 2050 and 2070 showed suitability potential as 3.62% (119,327.65 km(2)) and 4.29% (141,023.58 km(2)) by RCP 2.6, 4.41% (144,968.3 km(2)) and 3.98% (130,833 km(2)) by RCP 4.5 and 4.1% (134,777.7 km(2)) and 3.53% (116,040.38 km(2)) by RCP 8.5 respectively, compared to decline from current range 3.70% (121,765.26 km(2)) in the long term. The ancestral reconstruction by Mesquite v.3.70 showed bioclimatic variables linked to character states such as denticulate leaf margin, and fleshy fruits without horns or wings as ecologically informative character states in B. aborensis and as an indicator of the distribution of the species in heavy rainfall regions. [GRAPHICS]