Congenital aplasia of the major salivary gland is a rare condition. We report on a case of bilateral aplasia of the submandibular glands associated with a left submandibular hemangioma. A 62-year-old woman came to our department complaining of a 3-year history of left submandibular swelling. She had no notable family or personal medical history. On physical examination of the head and neck region, a 30 mm, non-tender mass was palpated in the left submandibular area. On imaging examinations including ultrasonography and CT, lack of the right submandibular gland and a left submandibular mass with calcification were demonstrated. Fine needle aspiration cytology resulted in blood elements only. Functioning tissue could not be observed in the bilateral submandibular glands on technetium pertechnetate scintigraphy. We performed a left submandibular tumor extirpation. Intraoperatively, the left submandibular gland and duct were missing. On pathologic examination, the tumor was found to be a hemangioma. The parotid and sublingual glands were recognized bilaterally on postoperative MRI. Her postoperative condition was satisfactory. This condition may be due to the dysfunction of several factors, such as fibroblast growth factors, related to gland differentiation.