Two new fairly complete remains of dogs were uncovered from a burial in Hayonim Terrace (northern Israel), dated to the first half of the 11th millenium (bp) (Late Natufian). This burial contained the remains of three humans associated with an elaborate construction. A detailed analysis of these dogs, and a comparison with all known Natufian remains, suggested that genuine dogs were already living around and within human habitations during this period. While most studies on early dogs were carried out on post-Natufian material, a period during which intentional selection could have already been widely experienced, we show that the evolvement of Natufian dogs were the product of unconscious selection of commensal wolves quasi-isolated under the special anthopogenic habitats created within and around Natufian sites, and at least ritually assimilated to human society. There is no evidence that Neolithic dogs are direct descendants of Natufian ancestors. Their multiregional origination is a widely accepted phenomenon. We suggest that Neolithic dogs were either domesticated anew, or were introduced from elsewhere to the southern Levant. Although the number of specimens of Natufian dogs is still small, evidently the emergence of some patterns clearly indicate that all them were already markedly different from the recent southern Levantine wolves and, in spite of their widely ranged morphology, constituted a unique group. It is shown that the shortening of the muzzle mainly affected the anterior part of the snout, while the posterior region remained practically unchanged. In this respect they seem to display a typical case of paedomorphosis. The simultaneous diminution of the carnassials, and other teeth, alongside with the snout, was marked enough that no crowding of the teeth took place by any of the Natufian dogs. The disproportional reduction of the snout versus teeth that caused the “crowding” phenomenon is only known from later periods.