The geographic borders between related species are often overlapping and much is unknown about the ecological and evolutionary dynamics between species in these regions. This is particularly true within long-lived forest trees such as conifers. The spruce species Picea glauca and Picea engelmannii were used in this study to elucidate the genetic dimension of their hybridization, as these species are ecologically divergent and are known to hybridize in nature. Opportunities for hybridization occur along elevational gradients where they co-occur, from northwestern Wyoming north through the central Rocky Mountains and British Columbia. This study was concentrated in the Central Rocky Mountains in Wyoming including the Greater Yellowstone Ecosystem. We found remarkable variation of genetic ancestry within and among geographic locations. Our genetic results provide evidence for a previously unrecognized, complex geographic mosaic for the interaction between these two species in this part of North America.