In sheep populations with small effective population sizes (Ne), inbreeding is a major concern because genetic variation has to be maintained. A panel of 28 microsatellite markers was used to measure the inbreeding level in three separate Merino flocks bred for superfine wool (CR), low parasite resistance (LR) or high parasite resistance (HR). The Ne was equal to 71.31, 19.19 and 19.48 in the CR, LR and HR flocks, respectively. Inbreeding levels estimated as inbreeding coefficients (FIS) were 0.019, 0.034, and 0.048 in the CR, LR and HR flocks, respectively. These values are quite low, being lowest in CR. This result is in contrast with the known relationship between small Ne and inbreeding level. The reasons could be the management practices in the CR flock of importing sires and restricting the policy of inbreeding by avoiding the mating between relatives. Thus, despite the small Ne and a very limited number of sires being used in every generation, these breeding practices seemed to be effective in avoiding inbreeding. The results reinforce the usefulness of microsatellite markers as a valuable instrument in various genetic aspects of sheep populations. It is suggested that these observations could be implemented with endangered species and breeds with small Ne, thus improving the effectiveness of correct breeding practices, even without direct measuring of genetic variation in populations.