Biological nitrogen fixation is one of the most critical processes contributing to ecosystem productivity and stability on a global scale. In temperate climates of the northern hemisphere, plant-root associated bacteria of the genus Frankia are the major nitrogen fixers in forest environments. Trees belonging to the genus Alnus are the most widespread hosts of Frankia in the Pacific Northwest, and a myriad of biotic and abiotic factors can influence the robustness of this symbiosis. Host identity and bacterial strain are important features that can impact Alnus-Frankia association, but little is known about the interplay of intrageneric hosts that co-occur in natural settings. In this study we investigated the genetic diversity and host specificity of Frankia bacteria associated with sympatrically occurring populations of Alnus rubra (red alder) and Alnus rhombifolia (white alder) in Oregon. Based on sequence analysis of the nifH gene recovered from root nodules we found low overall bacterial diversity. One dominant Frankia genotype was associated with both host species, indicating a lack of strong host specificity in this system. Our results suggest that certain intrageneric plant hosts with overlapping distributions show cross-compatibility with symbiotic actinorhizal bacteria, and that low strain diversity of these bacteria can persist across mixed host populations.