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In the 16th Century, the village of Vanara was an upcoming port. The Bandra hillock occupied a strategic point in the vicinity of the then enriching Mithi river and the sea, and Portuguese Jesuits wanted to make the best of it by placing a statue of the Mother Mary. Writes Msgr Francis Correa in his book, The Heritage of Mount Mary Bandra, "If Mary protects you, you will have nothing to fear..." With this assurance at the back of their minds, these priests selected the mount for the foundation of an oratory and placed a majestic statue of the Mother of God on the main altar. This oratory gradually developed into a Marian shrine and later, a minor Basilica.

The chapel was enlarged in 1678, by when the shrine had become a place of pilgrimage for Christians and non-Christians. A statue of the Mother was reportedly found floating in the sea between 1700 and 1760. It was first stationed as Our Lady of Navigators in St. Andrew's Church. However, in the early 1700s, Arab pirates disfigured the original statue of Mary of the Mount. When the church was rebuilt in 1760, the statue from St. Andrews was brought in. In 1761, the original, disfigured statue was renovated with a child in her arms and has been worshipped at the Bandra fair ever since.

In 1879, Jamsetjee Jeejeebhoy constructed a flight of steps from the foot of Mt. Mary hill to the north side of the church, known as the 'Degrados de Bomanjee'('Steps of Bomanjee').