With the end of the Nine Years' War in 1603, O'Dubhda territory, like that of other "rebels", could have been in jeopardy, but for the reluctance of King JamesVI & I to be too harsh, and the Treaty of Mellifont left things as they were. Donal O'Dubhda, brother of Tadhg Bui, looked after the interests of Daithi Rau's son, David while he was a minor and studying at Trinity College. After David came of age, the family formed into two distinct branches, the descendants of David using the surname O'Dowda, and those of Donal using O'Dowd. In 1656, there was a reunion as David O'Dowda married Dorothy O'Dowd.
Meanwhile, the Dublin branch of the family, that had moved away in the mid-15th century, had become influential in the capital. As merchants, they traded with England, reaching Chester and even London. In 1626, when Dublin merchants wished to bring their grievances to the attention of King Charles I, it as Alderman John Dowd who was chosen to present their case. The following year, Francis Dowd was elected Sheriff of Dublin and Master of the City Works.
During the early part of the century, the govrnment was happy to assist those wishing to emigrate and landowners often raised troops to fight for European rulers. In 1629, Col. Edward Dowd raied a regiment to fight for the King of Spain, but en route for the coast, decided to attempt to sack the City of Derry. His attack failed and he was hanged.