The death of Francis Willughby, on 3 July 1672, in his thirty-seventh year, was a blow to Ray more severe even than the loss of his fellowship at Cambridge. On the earlier occasion he had foreseen his fate and chosen it under the constraint of conscience but with open eyes. It had led to the formation of a plan and a partnership, the worth of which was tested and approved in the next decade. Now almost without warning the partnership was broken and the plan imperilled. Ray's feelings are revealed in the prayer that he offered in the family after its bereavement and in the noble Preface to the Ornithology: they are not less plainly shown in his refusal to abandon their joint purpose, in his acceptance of its fulfilment as a debt of honour to his dead friend, in the energy with which he took up the immediate task of caring for the children and perpetuating the work entrusted to his charge.

The loss of Willughby was inevitably irreparable. His portraits, the picture probably by Gerard Soest, engraved rather badly by Lizars, and the bust by Roubiliac in Trinity College, bear out the testimony of his partner.