This is the passenger and immigration list showing that a Samuel and Elizabeth Holly came to America in 1635. 

This document shows that a Samuel Holly purchased land in Cambridge, MA, in 1639, and died in late 1643.

A John Holly inherited Samuel and Elizabeth's land, which suggests that he was their son.  It also shows that Elizabeth died in 1645. 

This e-mail is from a genealogist, who has record that John Holly's parents were Samuel (b.1588) and Elizabeth.  The Samuel and Elizabeth who came to America in 1635 and settled in Cambridge, MA, were most likely John's parents.