This work intended to detect yeast species involved in sheep and goats respiratory infections using culturing method, biochemical auto-fluorescence technique and PCR assay. To realize this, 50 lung specimens and 50 samples of nasopharyngeal swabs were collected from clinically diseased sheep and goats freshly slaughtered animals in Kalyobia Governorate. These samples were subjected to fungal examination and the result showed that from the 50 examined sheep and goats lung, 21 lung (42%) had yeast infection and out of 50 nasal swab from sheep and goat 16 (32%) had positive yeast. The architectural detail of bright green-to-yellow green auto-fluorescence spherules, yeast forms Cryptococcus gave stronger and brighter fluorescence it is known to be fast test used in detection to mycotic pneumonia with any late accompanied by  haematoxylin and eosin stain (H&E) staining. PCR results proved that Cryptococcus isolates were positive, where for the results of PCR proved that only 3 (17.6%) isolates were positive for Cryptococcus albidus. Considering of this fact this study suggest screening and detecting fungal species using of auto-fluorescence methods and PCR technique in pneumonic sheep and goats.