Stripe rust is the most important disease of wheat in Ecuador. Knowledge of race diversity of the pathogen population is limited. Here we present avirulence/virulence phenotypes found in Pst samples collected from wheat between 2001 and 2014. A total of 30 isolates from the Ecuadorian highlands were tested on 15 near-isogenic wheat lines carrying single resistance genes; 21 races were identified. Lines with Yr2, Yr3, Yr26 and Yr27 were not tested in some years. Virulences to Yr1, Yr6, Yr7 and Yr9 were the most frequent (over 70%) in all years, followed by virulence to Yr17 (67%) and Yr27 (53%). Virulence to Yr8 was not found in 2013 and 2014. Virulence to Yr24/Yr26 was present in each year except 2014, although at a low level. Virulence to Yr10 was low. There were some unconfirmed discrepancies from a perfect association of virulences to Yr24/Yr26 and Yr10. Virulence to YrSP increased up to 2013, but was absent in 2014. There was no virulence to Yr5 and Yr15. Despite limited sampling, a diverse population of Pst seems to be present in Ecuador, with virulence for most resistance genes being present. Based on these analyses resistance to Pst in Ecuador could be achieved with Yr5 and Yr15, together with Yr24Yr26, and perhaps YrSP. One possibility for the high pathogenic variation might be sexual recombination on one or more of the 32 Berberis species reported in Ecuador. This needs to be examined along with more intensive sampling from wheat and analysis of the actual resistance genes present in current cultivars.