Around 1563 Lopes married Sarah Anes (b. 1550), the eldest daughter of another New Christian refugee from the Portuguese Inquisition, the merchant Dunstan Anes, who had settled in London in 1540. According to Samuel, both the Anes and Lopes households secretly practised Judaism, which was then illegal in England, while outwardly conforming as Anglicans. Other scholars are ambivalent on the matter; Lopes would always insist that he was a Christian. Roderigo and Sarah had four sons and two daughters, of whom at least the eldest five—Ellyn (Elinor), Ambrose, Douglas, William and Ann—were baptised within the hospital precincts at St Bartholomew-the-Less between 1564 and 1579. Lopes' brother Lewis lived with them in Holborn; a second brother, Diego Lopes Aleman, became a merchant in Antwerp and Venice.