The chromatin remodelling proteins DAXX and ATRX are key regulators of genome stability and epigenetic processes. Alterations in their expression have been associated with tumour stage and prognostic outcomes in various human cancer types, whereas their role in veterinary oncology has received little investigation to date. We analysed canine prostate and urinary bladder samples, including 18 prostate carcinomas (12 adenocarcinomas and 6 prostatic urothelial carcinomas), 10 non-malignant prostate tissues, 22 urinary bladder carcinomas, and 6 non-malignant bladder tissues. Nuclear expression of DAXX and ATRX was assessed using fully quantitative digital immunohistochemistry. Overall, DAXX exhibited consistently higher expression than ATRX across benign and malignant samples from the prostate and bladder. DAXX and ATRX expression demonstrated a positive correlation across all samples (ρ = 0.553, p < 0.05), suggesting coordinated regulation. They displayed organ-specific expression patterns: prostate carcinomas showed increased expression of DAXX compared with non-malignant prostate tissues (p < 0.05). In contrast, in the bladder, expression of DAXX and ATRX declined with increasing tumour grade (p < 0.05). Our findings provide new insights into the potential of DAXX and ATRX as biomarkers, offering new insights into their clinical relevance in dogs.