We examined the long-term effects (28 years) of habitat loss and phenotype-based selective harvest on body mass, horn size, and horn shape of mouflon (Ovis gmelini musimon) in southern France. This population has experienced habitat deterioration (loss of 50.8% of open area) since its introduction in 1956 and unrestricted selective hunting of the largest horned males since 1973. Both processes are predicted to lead to a decrease in phenotype quality by decreasing habitat quality and by reducing the reproductive contribution of individuals carrying traits that are targeted by hunters. Body mass and body size of both sexes and horn measurements of males markedly decreased (by 3.4-38.3%) in all age classes from the 1970s. Lamb body mass varied in relation to the spatiotemporal variation of habitat closure within the hunting-free reserve, suggesting that habitat closure explains part of these changes. However, the fact that there was no significant spatial variation in body mass in the early part of the study, when a decline in phenotypic quality already had occurred, provided support for the influence of selective harvesting. We also found that the allometric relationship between horn breadth and horn length changed over the study period. For a given horn length, horn breadth was lower during the second part of the study. This result, as well as changes in horn curve diameter, supports the interpretation that selective harvesting of males based on their horn configuration had evolutionary consequences for horn shape, since this phenotypic trait is less likely to be affected by changes in habitat characteristics. Moreover, males required more time (approximately four years) to develop a desirable trophy, suggesting that trophy hunting favors the reproductive contribution of animals with slow-growing horns. Managers should exploit hunters' desire for trophy males to finance management strategies which ensure a balance between the population and its environment. However, for long-term sustainable exploitation, harvest strategy should also ensure that selectively targeted males are allowed to contribute genetically to the next generations.