There are references to the “Phoenix,” a Dutch ship taken as a prize, among the State Papers (see “Calendar,” 1666-67, p. 404). Pepys appears to have got into trouble at a later date in respect to this same ship, for among the Rawlinson MSS. (A. 170) are “Papers relating to the charge brought against him in the House of Commons in 1689 with reference to the ship Phoenix and the East India Company in 1681-86.”
This text comes from a footnote on a diary entry in the 1893 edition edited by Henry B. Wheatley.