The article presents on the presence of pipistrelle bats, Pipistrellus and Hypsugo, in Sardinia, Italy. The study explores the variability of pipistrelles on the island, which is known for its comparatively high degree of endemism, including cryptic diversity. It examines the species occur on the region through developing Bayesian phylogenetic trees and minimum spanning networks and provide description on the affiliations of the evolutionary lineages. It identifies five pipistrelle lineages on the island, which include Pipistrellus pipistrellus, Pipistrellus pygmaeus, and Pipistrellus desertii. It also suggests a high pipistrelle diversity in the island compared to any other Mediterranean island.