An outbreak of mortality in a breeding facility of European Pond Turtles (Emys orbicularis) in the Ebro Delta (Tarragona, Spain) occurred in 2014-2015. The breeding program began in 2006 and has generated up to 250 turtles every year. They are released when they are 4 to 5 years old. After a change of the diet of the turtles born during 2014-2015, a mortality of 91% (334 out of 366 animals) was calculated for the hatchlings from 2014. Clinical signs were soft shells, apathy and anorexia approximately 1-5 days before death in all affected turtles. Histologically, thyroid follicles were lined by hypertrophic columnar epithelium and follicular lumina were mostly devoid of colloid. Kidneys were also affected, showing mild to moderate acute degeneration and tubular necrosis with mineralization of tubular epithelium. Stenotrophomonas maltophilia was isolated in pure culture from tissue pools of tested animals. PCRs sensitive for detection of ranavirus, herpesvirus and coccidia (spp.) were all negative. Thus, we conclude that the high mortality outbreak was associated with a thyroid gland hyperplasia and renal malfunction due to a change in diet, complicated with an opportunistic secondary bacterial infection