Loud acoustic signals of mammals may contain information about their progenitors. There is a question whether such phenomenon is possible to expect in domestic animal breeds as well, since the time of breed establishment has been a rather long one. Therefore we tested whether a significant morphological distinction of a newly established horse breed and its important founding contributor differed in their vocalization. We analyzed 304 whinnies of 35 individual horses (197 whinnies of 23 individuals belonging to Czech Warmblood and 107 calls of 12 Thoroughbreds). Despite of the fact that the two breeds differed significantly in most of their morphological measurements (height at withers, thoracic perimeter, cannon bone perimeter, and body weight), they did not differ in any of the measured acoustic parameters (both frequency and temporal ones). Our results indicate that morphological distinction of Thoroughbred and Czech Warmblood was not accompanied by distinct vocalization.