Neurergus kaiseri ,native to Iran, is a threatened pond-breeding newt species distributed insouthern ranges of the Zagros Mountains. In spite of several potential threats such as habitat loss, climatechange and drought, there are limited studies about Lorestan newt habitatrequirements and their effects on its genetic differentiation. In the first part ofthe study, we estimated potential area of occupancy ofthis species as a measure of its geographic range using a multi-stagedistribution modelling. Climatic and habitat variables were characterisedrespectively at landscape (coarse-grained) and local spatial (fine-grained)scales in Maxent to model the distribution range of each of the two recognisedclades of the species, separately. To approximate the species area ofoccupancy, we modelled the potential distribution of springs as the specificaquatic habitat of N. kaiseri across its geographic range and masked themodelled fine-grained distribution range of the species with the potentialdistribution map of springs. Landscape-scale variables were more determinativefor the northern clade’s presence, whereas local-scale variables were moreimportant for the southern clade. The species suitable habitat area obtained bylocal-scale models was approximately 90% less than the predicted potentialdistribution obtained by climatic landscape-scale models. The area of occupancyof the species was estimated 620 km 2 showing approximately a 20%reduction in the predicted habitat area by the local-scale model. In the second part, we explored therelative contributions of ‘geographic distance’, ‘landscape resistance’ and‘environmental resistance’ on variations of mitochondrial D-loop and nuclear genome inthe species populations, tested level of intra-specific phylogenetic nicheconservatism, and studied local scale ecological characterization of thespecies breeding habitat. We used a mitochondrial marker (i.e. D-loop) and agenome-wide restrictionsite-associated DNA sequencing (RADseq) database (i.e. single nucleotide polymorphisms; ) to investigate the genetic structure of of N. Kaiseri ’spopulations and identify factors affecting its populations’ genetic differentiation. We detectedeight haplotypes within 17 populations based on mtDNA that diversified into twoclades that geographically disconnected by Dez River. The same pattern ofcladogenesis was detected based on dataset. Genetic variation between thetwo clades located on two sides of Dez River was 81.87% based on mtDNA and76.62% based on , implying that the river was acted as a barrier to geneflow. Environmental dissimilarity, followed by Geographic distance contributedmost to mtDNA differentiation of N. kaiseri ’s populations. However,based on dataset, isolation by river, followed by isolation by distancehad a significant influence on genomic variation in Kaiseri’s newt. AMOVA andPCA, beside landscape genetic analysis, supported the role of Dez River in thepopulation divergence within N. kaiseri and shaping the distribution ofnorthern and southern clades. There was a significant difference betweenclimatic niche belonging to each clade but based on local-scale habitatvariables the two niches were equivalent. The “niche similarity analysis”supported niche conservatism hypothesis. A southward shift in the southernclade’ climatic niche was detected. Niche conservatism and environmentalconstraints interactions have resulted in creation of non-equivalent climaticniches, yet equivalent local spaces. In the third part, ecologicalcharacteristics of the breeding sites were investigated at the local spatialscale. To identify key factors affecting the breeding site selection by N.kaiseri , we compared ecological characteristics of 20 occupied with 20unoccupied springs by the species using 13 habitat variables in the breedingseason. Bed type, water flow rate, shading area, and dissolved oxygen were themost important factors in occupying water-bodies by Kaiser’s newt. Thelikelihood of species presence was comparatively higher in sites with slowwater flow, high dissolved oxygen, cobble substrate, and high shading area.Habitat alteration may highly affect physical-chemical characteristics of thespecies breeding habitat, and hence the probability of its occurrence. Thenovel procedure used in this study for approximating area of occupancy ofKaiser’s newt can be used for estimating area of occupancy of other similarspecies. In addition, by assessing landscape- and local-scale environmentalconditions, our study provides a basis for predicting species’ response toclimate change. Keywords: Speciesdistribution modelling, Landscape genetics, Local habitat, Kaiser’s newt, Areaof occupancy