The great sensitivity of amphibians to land disturbance is one of the main causes that contributed to their worldwide decline. One fundamental approach in assessing amphibian ability to reflect habitat degradation is to measure their phenotypic changes in contrasting environments. We examined the extent to which several morphological traits of the endemic anuran Pelophylax perezi responded to agricultural conversion in Monegros, an arid region in NE Spain. Specifically, we determined how body size, body mass, body condition (BC) and fluctuating asymmetry (FA) of different frog classes varied among habitats with different degree of management, i.e. rice fields vs. control ponds (i.e. small reservoirs). Pelophylax perezi juveniles showed a decrease in size and mass in rice fields, revealing that early life stages are generally more susceptible to habitat alteration. Adult body condition, on the other hand, increased significantly in cultivated habitats, which apparently indicates a good fitness in this size class. Nonetheless, skeletal asymmetry of both, juveniles and adults was significantly higher in rice fields. Moreover, during postmetamorphic development FA increased significantly towards adult stage indicating that the development controlling mechanisms were not able to buffer the stress induced by land use change. Among traits, humerus, radio-ulna and metatarsal were highly sensitive in terms of expressing significant FA differences between habitats, contrary to tibio-fibula, whose precise symmetry is essential for animal locomotion. The former bones have therefore the potential to be used as sensitive indicators of stress in amphibians. FA showed no relationship with body condition. This, together with the previous results demonstrates that FA is able to capture habitat stress more reliably than the morphological estimates such as body size, mass and BC. Therefore, FA is a useful morphological tool, highly recommended to monitor stress levels in amphibian populations.