Approximately 250 well-preserved conifer cones were recovered from late Tertiary sediments on Banks Island, Northwest Territories, Canada. We collected fossil cones from mid-Miocene autochthonous peat deposits in the Ballast Brook Formation. We also sampled overlying fossil-rich Pliocene fluvial deposits of the Beaufort Formation. For individual cones, we measured cone length, cone width, scale length, scale width, bract length, and where possible seed length. Numerous cones recovered from the Ballast Brook Formation sediments closely resemble extant Pinus, including at least two distinct species in the hard and soft pine sub-genera. The length to width ratio best discriminated hard pines (l/w = 1.49) from soft pines (l/w = 2.86). The morphology of the other cones suggests a close affinity to extant members of the genus Picea. These fossil cones were categorized into three distinct size classes based on their length to width ratios (l/w of 2.15, 2.49, and 3.23) indicating three possible species of Picea in our data set. Interestingly, Pinus and Picea frequently co-occur in the Ballast Brook Formation peat suggesting these species mutually existed in the high-latitude backswamp forest communities of which no modern analog exists today. However, Pinus and Picea cones co-occur less frequently in the Pliocene Beaufort sediments. This may reflect a change in high-latitude forest community composition from the mid-Miocene to the Pliocene coincident with climatic cooling.