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Simple Summary: The genus Crocidura has ~200 species, which accounts for roughly half of the Soricidae family's diversity. The "pergrisea" species group, which comprises at least four species—Crocidura arispa, Crocidura pergrisea, Crocidura ramona, and Crocidura serezkyensis—is especially interesting among Crocidura endemics of central and western Asian regions. The taxonomic value of a fifth species, Crocidura armenica, has been unclear for a long time owing to the poor condition of the skulls of both type specimens. Using a microcomputed-tomography-based cybertaxonomic (CTtax) approach and a newly developed pipeline, "AProMaDesU", we re-evaluated the type material of the Armenian shrew and expanded the hypodigm of this species using three additional specimens. A morphospace analysis based on three-dimensional craniomandibular datasets revealed the uniqueness of C. armenica and C. arispa. The extraction of museum DNA from a unique collection of samples of the "Crocidura pergrisea" species complex, which comprises local endemics of Central and West Asia, allowed us to determine their inter- and intragroup relationships. The first step of this study was the re-evaluation of heavily damaged type specimens of C. armenica via a microcomputed-tomography-based cybertaxonomic approach (CTtax), which enabled a precise description of the species' morphology; three-dimensional models of the cybertypes were made available through the MorphoBank Repository. We developed the "AProMaDesU" pipeline on the basis of five requirements for micro-CT-based cyber-datasets in relation to mammalian collections. Our second step was a combination of several meticulous approaches to morphological investigation against a background of a cytb-based phylogeny, which helped us to make a taxonomic decision about the status of species of the "pergrisea" group, e.g., C. arispa, C. armenica, and C. serezkyensis, when the morphological results were partly incongruent with the molecular phylogeny. Nevertheless, under two assumptions, our findings preserved a separate species-level status of C. serezkyensis and C. arispa. In addition, we restored the species-level status of C. armenica. This taxonomic decision is based on our morphospace analysis, which revealed unique craniomandibular shape transformations within the rocky shrews that helped them with the transition to a new area of morphospace/trophic niches and consequently separated them from the other analyzed Crocidura groups. [ABSTRACT FROM AUTHOR]