Climate change, as an emerging phenomenon, has led to changes in the distribution, movement, and even risk of extinction of various wildlife species and this has raised concerns among conservation biologists. Different species have two options in the face of climate change, either to adopt or follow their climatic niche to new places through the connectivity of habitats. The modeling of interpatch landscape communications can serve as an effective decision support tool for wildlife managers. This study was conducted to assess the effects of climate change on the distribution and habitat connectivity of the endangered subspecies of Asian black bear (Ursus thibetanus gedrosianus) in the southern and southeastern Iran. The presence points of the species were collected in Provinces of Kerman, Hormozgan, and Sistan-Baluchestan. Habitat modeling was done by the Generalized Linear Model, and 3 machine learning models including Maximum Entropy, Back Propagation based artificial Neural Network, and Support Vector Machine. In order to achieve the ensemble model, the results of the mentioned models were merged based on the method of “accuracy rate as weight” derived from their validation. To construct pseudo-absence points for the use in the mentioned models, the Ensemble model of presence-only models was used. The modeling was performed using 15 habitat variables related to climatic, vegetation, topographic, and anthropogenic parameters. The three general circulation models of BCC-CSM1, CCSM4, and MRI-CGCM3 were selected under the two scenarios of RCP2.6 and RCP8.5 by 2070. To investigate the effect of climate change on the habitat connections, the protected areas of 3 provinces were considered as focal nodes and the connections between them were established based on electrical circuit theory and Pairwise method. The true skill statistic was employed to convert the continuous suitability layers to binary suitable/unsuitable range maps to assess the effectiveness of the protected areas in the coverage of suitable habitats for the species. Due to the high power of the stochastic forest model in determining the importance of variables, this method was used. The results showed that presence/absence models were successful in the implementation and well distinguished the points of presence and pseudo-absence from each other. Based on the random forests model, the variables of Precipitation of Driest Quarter, Precipitation of Coldest Quarter, and Temperature Annual Range have the greatest impact on the habitat suitability. Comparing the modeling findings to the realities of the species distribution range indicated that the suitable habitats are located in areas with high humidity and rainfall, which are mostly in the northern areas of Bandar Abbas, south of Kerman, and west and south of Sistan-Baluchestan. The area of suitable habitats, in the MRI-CGCM3 (189731 Km2) and CCSM4 (179007 Km2) models under the RCP2.6 scenario, is larger than the current distribution (174001 Km2). However, in terms of the performance of protected areas, the optimal coverage of the species by the boundary of the protected areas, under each of the RCP2.6 and RCP8.5 scenarios, is less than the present time. According to the electric circuit theory, connecting the populations in the protected areas of Sistan-Baluchestan province to those in the northern Hormozgan and the southern Kerman would be based on the crossing through the heights of Sistan-Baluchestan and Hormozgan provinces and the plains between these heights would be the movement pinch points under the current and future scenarios. Populations in the protected areas of Kerman have higher quality patch connections than that of the other two provinces. The areas such as Sang-e_Mes, Kouh_Shir, Zaryab, and Bahr_Aseman in Kerman Province and Kouhbaz and Geno in Hormozgan Province can provide suitable habitats for the species in the distribution models. The findings revealed that the conservation of the heights along with the caves inside them could be a protective priority to counteract the effects of climate change on the species.