Microsporidia are obligate, intracellular fungi. In reptiles, they are most commonly reported in squamates. We report the first detection of microsporidiosis in inland bearded dragons (Pogona vitticeps) from Australia, and for the first time, mixed infections of microsporidium and adenovirus in asymptomatic inland bearded dragons. In one collection there were five individuals, one of which was lethargic, inappetent, and had lost weight. Two large ovarian granulomas were palpated (42 × 23 mm and 26 × 19 mm) and were surgically removed. This animal died shortly after surgery. Histological evaluation of these granulomas revealed granulomatous inflammation within or adjacent to ovarian tissue, containing numerous aggregates of microorganisms consistent with microsporidia. The organisms were confirmed as Encephalitozoon pogonae by polymerase chain reaction (PCR) and sequencing. Agamid adenovirus-1 was also detected. These two infectious agents were also detected by PCR in all the other bearded dragons in this collection (n = 5), all of which were asymptomatic. A single dragon from a second collection presented for a routine wellness examination after the sudden death of another dragon in the collection. This dragon had similar intracelomic masses to the dragon from the first collection. These were removed surgically, but the dragon died 5 wk later following 3 wk of treatment with 25 mg/kg fenbendazole PO q7 days. Necropsy samples were collected and the microsporidian Encephalitozoon pogonae was detected in oral–cloacal swabs, blood, and multiple tissues by PCR and sequencing. Agamid adenovirus-1 was not detected in this dragon.