The combination of intravital dye, methylene blue (MB), with molecular cancer marker, pH low insertion peptide (pHLIP) conjugated with fluorescent Alexa532 (Alexa532‐pHLIP), was evaluated for enhancing contrast of pathological breast tissue ex vivo. Fresh, thick breast specimens were stained sequentially with Alexa532‐pHLIP and aqueous MB and imaged using dual‐channel fluorescence microscopy. MB and Alexa532‐pHLIP accumulated in the nuclei and cytoplasm of cancer cells, respectively. MB also stained nuclei of normal cells. Some Alexa532‐pHLIP fluorescence emission was detected from connective tissue and benign cell membranes. Overall, Alexa532‐pHLIP showed high affinity to cancer, while MB highlighted tissue morphology. The results indicate that MB and Alexa532‐pHLIP provide complementary information and show promise for the detection of breast cancer.