The striped dolphin (Stenella coeruleoalba) is the most abundant cetacean inhabiting the Mediterranean Sea and is considered genetically and morphologically distinct from Atlantic conspecifics. Although a common species, the underwater acoustic behaviour of the striped dolphin has been studied very little. This study is the first to characterize the whistle repertoire of this species. Extensive field recordings were made from May to October 2007. Acoustic parameters were measured for 1738 whistles and contour categories (or calls) were assigned. Microgeographic variation in whistles was analyzed for inshore, slope, and offshore ecological habitats in the Ligurian Sea using single factor analysis of variance and Homoscedastic-Canonical Discriminant Function Analysis. Frequency of the calls ranged from 1.4 to 24.0 kHz, with a mean Center Frequency of 10.6 ± 1.9 kHz and a short average Inter Quartile Ratio duration of 0.34 ± 0.19 s. When categorized, the whistle repertoire consisted mostly of sine 28%, convex 27%, upsweep 14% and concave 14% calls. Geographic variation of acoustic features of whistles was identified among inshore, offshore, and slope areas. Based on prior genetic analysis, striped dolphins are found in these three distinct ecological habitats of the Ligurian Sea and individuals may not associate often to avoid direct competition for prey. Furthermore, this analysis of acoustic features of whistles supports the existence of three geographically distinct groups of this species.