Only a few is known about alarm calls of the European ground squirrel (Spermophilus citellus) (EGS) and the recently described Taurus ground squirrel (S. taurensis) (TGS). The aim of our study was to conduct detailed analysis and comparison of calls in these species. We also tested the potential of calls to code information about callers´ identity. Calls were recorded during summer 2007 and 2008 in colony of EGS in Prague, Czech Republic and in colony of TGS near Akseki, Turkey. Recorded calls were emitted toward humans by individuals sitting in entrances of their burrows. 600 calls (30 per individual) from 20 individuals (10 per species) of the EGS and the TGS were analyzed. In both species, alarm calls are tonal sounds usually consisting of two different elements. Both species significantly differ in several spectral and temporal parameters. Discriminant analysis classified more than 96 % of calls to a correct species. Calls in the EGS as well as in TGS were highly individually distinct. Discriminant analysis correctly classified 98 % of calls in the EGS and 94 % of calls in the TGS. Acoustic analysis revealed that the EGS and the TGS can be distinguished on the basis of their calls and support conclusions that vocalizations represent good features supporting species designations. We also established a big potential to recognize individuals on the basis of acoustic structure in their calls. Supported by the Ministry of the Environment of the Czech Republic (grant No. VaV/620/1/03 and No. SP/2d4/61/08).