The fossil remains of the genus Pinus are common in the European Paleogene and Neogene record. Apart from seed cones, most of the vegetative remains are difficult or even impossible to accurately classify in the modern systematic schemes of the genus. In the late Miocene assemblage of Pitsidia (Messara Basin, southern Crete) Pinus and Myrica remains dominate with thousands of vegetative and fertile specimens. The outcrop comprises a 4.5 to 5.0m thick sequence of silts and sands, rich in plant fossils. The exceptional preservation of some specimens provides significant micro-morphological and anatomical details of taxonomic value. The Pitsidia pine remains include dwarf shoots, long shoots, isolated needles, fascicle bracts, bud scales, male cones, isolated scales of male cones, seeds and ovulate cone scales. We were able to classify the material to at least subgenus and in some cases section. Both subgenera Pinus and Strobus occur in the assemblage. Concerning the dwarf shoots, three different pine species were identified, Pinus sp. – two-needled fascicles (subgen. Pinus), Pinus sp. – five-needled fascicles (subgen. Strobus) and the proposed new species Pinus pitsidiensis (subgen. Pinus) for the abundant three-needled fascicles. Lastly, we reconstruct the whole plant of P. pitsidiensis sp. nov. and discuss its paleoecology.