In Portugal, donkeys represent a large legacy of social, cultural, economic and ecological importance. The only native breed of donkeys, the Miranda Donkey, is composed by a small number of animals. The aim of this study was to evaluate the parasitic infection, particularly the variation in the rate of positivity, the level of parasitic infection (LPI) and the biodiversity of intestinal parasites in a population of 62 Miranda donkeys, exposed to an anti-parasitic control every 6 months, with subcutaneous injection of ivermectin 2% at the dosage of 1 ml/50 Kg BW, between July 2005 and February 2010. During this period, there was a decrease in the positivity rate, from 87% (54/62) in 2005 to 32% (20/62) in 2010, as well as a decrease in the LPI. In 2005, 70,4% of the infected animals had levels higher than 1000 eggs per gram (EPG), considered a high LPI and in 2010, 75% of the infected animals had levels under 500 EPG, low LPI. Biodiversity also decreased during this period, namely the decrease of Strongylinae in relation to Cyathostominae. Considering that consistent levels of parasitic infection are still observed in this population and that the most observed Strongylidae are the ones of genus Cyathostomum sensu latum, these results are worrying because these agents are frequently referred by its ability to acquire resistance to anti-parasitic drugs.