The Persian dwarf snake Eirenis (Pseudocyclophis) persicus (Anderson, 1872) has a wide distribution range in south-western Asia. This species group was comprehensively studied here using traditional biometry, geometric morphometrics, ecological niche modelling, and genetics. Our analyses revealed that E. persicus is split into two clades. A western clade, bearing at least two different species: E. persicus, distributed in south-western Iran, and an undescribed species from south-eastern Turkey and western Iran. The eastern clade consists of at least three species: Eirenis nigrofasciatus, distributed across north-eastern Iraq, and western and southern Iran; Eirenis walteri, distributed across eastern Iran, southern Turkmenistan, and western and southern Pakistan, and Eirenis angusticeps, distributed in north-eastern Pakistan. Ecological niche modelling revealed that the distribution of the species in the western clade are mainly affected by winter precipitation, and those in the eastern clade are mainly affected by the minimum temperature of the coldest month. A molecular clock analysis revealed that the divergence and diversification of the E. persicus species group mainly correspond to Eocene to Pliocene orogeny events subsequent to the Arabia–Eurasia collision. This study confirms that specimens with the unique morphology of having 13 dorsal scale rows on the anterior dorsum, occurring in the Suleiman Mountains in central Pakistan, can be referred to Eirenis mcmahoni (Wall, 1911). However, at this moment we have insufficient data to evaluate the taxonomy of this species.