Previously, we found that dogs belonging to the herding breed group, selected for human cooperation, synchronise their long-term stress levels with their owners. The aim of the current study was to investigate features that could influence long-term stress levels in ancient dog breeds, genetically closer to wolves, and dogs specifically selected to work independently of their owner. Twenty-four ancient breed dogs and 18 solitary hunting dogs were recruited and hair samples were obtained from both dogs and owners from which hair cortisol concentration (HCC) was analysed. Additionally, the owners completed lifestyle surveys, the Monash Dog Owner Relationship Scale (MDORS) on human-dog relationship, and both dog and owner personality questionnaires (Dog Personality questionnaire and Big Five Inventory survey). The results from the MDORS indicate that the subscale Perceived cost correlated to the dog HCC of tested breed groups: solitary hunting breeds (χ = 4.95, P = 0.026, β = 0.055), ancient breeds (χ = 2.74, P = 0.098, β = 0.027), and herding dogs included from a previous study (χ = 6.82, P = 0.009, β = - 0.061). The HCC of the solitary hunting dogs was also related to the owner personality traits Agreeableness (χ = 12.30, P < 0.001, β = - 0.060) and Openness (χ = 9.56, P = 0.002, β = 0.048) suggesting a more substantial influence of the owner on the solitary hunting dog's HCC compared to the ancient breeds. No effect of owner HCC on dog HCC was found in either ancient or in solitary hunting breeds. Hence, the long-term stress synchronisation is likely to be a trait in breeds selected for human cooperation. In conclusion, dog HCC is often related to the owners' personality, but is primarily influenced by the owner-dog relationship.