Colonel Sir John Lowther (c. 1628 – March 1668) was an English landowner, at Hackthorpe, the eldest son and heir of Sir John Lowther, 1st Baronet and Mary Fletcher.
He first married, in 1665, Elizabeth Bellingham, daughter of Sir Henry Bellingham, 1st Baronet. They had two children:
By his second marriage to Mary Withins, he had one (posthumous) son:
He predeceased his father and did not succeed to the baronetcy.