We investigated the troglobiont biodiversity of Iran, with a focus on Zagros karstic areas. This study followed three main goals. First, a discovery component involved faunistic investigations into the troglobiont organisms in Zagros Mountains of Iran, as well as taxonomic descriptions of new taxa. Three new troglobiont species were described: a carabid beetle, an asellid isopod and a truncatelloid gastropod. Additionally, we report on the discovery of six species under description (Oligochaeta, Decapoda, Isopoda) and over 10 species that are awaiting description. DNA extraction and PCR of selected markers from most of these taxa have been done, enabling species delimitation and phylogenetic analyses. We recorded new habitats for previously described Iranian cave fishes. Our second aim was to examine patterns of troglobiont biodiversity and endemism in the Zagros Mountains of Iran. We published a checklist of Iranian subterranean arthropods in 2017. In an additional chapter, we listed all Iranian troglobiont animals (previously published and our new discoveries, including yet undescribed species). The species richness and distribution patterns of Iranian troglobiont diversity were presented, including one currently recognized biodiversity hotspot. As the third goal, we aimed to analyze Iranian troglobiont animals phylogenetically to understand their relationships and to identify their origin and estimate a timeframe for their colonization into subterranean habitats. The new troglobiont species and some of sampled surface relatives were used for DNA isolation and molecular analysis. Related sequences were mined from GenBank. Given the poor knowledge of Iranian subterranean fauna, this speleobiological dissertation enriched this knowledge by reporting new findings and describing new species. The discovery component of this thesis enabled us to establish Iran as an important part of the world map of subterranean biodiversity. We now understand more about the origins of Iranian troglobionts and the time of their adaptation to subterranean environment. This fauna is likely to show high endemism and is important from the conservation perspective.