A case of disseminated pseudallescheriasis in a German Shepherd bitch is presented. Bones (ilium, a rib and phalanges), joints (elbow and acetabulum) and the surrounding tissues were the principal organs affected. In addition, Pseudallescheria boydii was isolated, in lower numbers, from the eye, kidney, lymph nodes draining the affected regions and urine. The dog was euthanized. P. boydii was identified by morphologic characteristics and molecular techniques (beta tubulin sequence). In addition, an ITS nucleotide sequence analysis showed that this strain differed from another isolate identified as Scedosporium apiospermum that had caused a disseminated infection in another German Shepherd. The importance of the molecular characterization of fungi belonging to the Pseudallescheria/Scedosporium complex, isolated from animals is stressed in light of the ongoing attempts to recharacterize these fungi.