Behavioral and physiological responses of Kangal dogs in different livestock flocks; i.e. sheep and goat flocks, which are the most frequently guarded livestocks by those dogs, were examined in the present study. Salivary cortisol levels and the values of behavior were examined three different times from each dog, namely while they were resting around the house or the pen, when dogs confronted with the flock and when dogs guarded the flock in the pasture. The maximum cortisol levels of dogs confronted with goats significantly higher than the confronted from sheeps (p < 0.05). Accordingly, it can be suggested that confrontation with the goat flock is more stressful comparing with the sheep flock. However, no significant difference was found, when comparing maximum cortisol values during the active protection in sheep flock and goat flock. Moreover, no statistical difference was found when comparing the direct behavioral reactions of the dogs during the confrontation with the sheep and the goat flocks. Considering "hyperactivity" and "low tail position" behaviors of Kangal dogs during the active guarding of the flock, statistically significant differences were found between the sheep and goat flocks (t-test: p < 0.01). Thus, one may argue that Kangal dogs feel less secure in the goat flock in comparison to the sheep flock.