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Rh Thirteen of the thirty-one beds of lignite which were cut through, and two of the beds of clay, yielded distinguishable plant remains. These were sent to Dr. Oswald Heer, of Switzerland, for examination; and he determined from the collection fifty species, including ferns, conifers, figs, cinnamon trees, an oak, a laurel, vines, andromedas, a bilberry, a gardenia, a water lily, and some leguminous plants. Heer referred the group to the Lower Miocene period, but some modification was afterward made in this determination in the light of a fuller knowledge of the Tertiary flora. The deposits and work at Bovey Tracey were the subject of a memoir to the Royal Society by Sir Charles Lyell; and Dr. Heer's account of his work—The Fossil Flora of Bovey Tracey—was published in 1863.

While this investigation was going on, Lyell was preparing the fifth edition of his Manual of Geology. He invited Pengelly to suggest corrections to the text, saying that, besides positive mistakes, he would "be glad of any hints and suggestions made freely, which your knowledge of the manner in which beginners are struck may enable you to send us." The criticisms supplied by Mr. Pengelly were adopted by Lyell except where they had already been made unnecessary.

On the accidental discovery by workmen, in 1858, of a cavern in Windmill Hill, overhanging the town of Brixham, Pengelly at once thought of finding what was in it, and what story it might have to tell. He visited the place and applied to the owner for permission to explore it in behalf of the Torquay Natural History Society. But on consultation with Dr. Hugh Falconer it was decided that as that society probably had not means sufficient to bear the expense of the exploration, the Royal and Geographical Societies should be applied to for a grant. This was obtained, and the work was carried on under the superintendence of Professor Prestwich and Mr. Pengelly, on whom, as a resident of the place, the burden substantially fell. The decision to explore the cave was brought about largely by the fact that it was a virgin cave which had been inaccessibly closed during an incalculably long period, the last previous event in its history having been the introduction of a reindeer antler, which was found attached to the upper surface of the stalagmitic floor. It was therefore free from the objection urged against Kent's Cavern that, having been long known and open, it had probably been ransacked again and again. A thorough method of exploration was determined upon, beginning with the examination and removal of the stalagmitic floor; after which the upper bed should be dealt with in a similar manner horizontally throughout the entire length of the cavern, or so far as practicable; then the next lower bed, and so on, till all the deposits had been removed. By this method the general