Dogs exhibit an exceptional range of morphological diversity as a result of their long-term association with humans. Attempts to identify when dog morphological variation began to expand have been constrained by the limited number of Pleistocene specimens, the fragmentary nature of remains, and difficulties in distinguishing early dogs from wolves on the basis of skeletal morphology. In this study, we used three-dimensional geometric morphometrics to analyze the size and shape of 643 canid crania spanning the past 50,000 years. Our analyses show that a distinctive dog morphology first appeared at about 11,000 calibrated years before present, and substantial phenotypic diversity already existed in early Holocene dogs. Thus, this variation emerged many millennia before the intense humanmediated selection shaping modern dog breeds beginning in the 19th century.