Alders (Alnus spp.) are important components of northern ecosystems due to their ability to fix nitrogen (N) in symbiosis with Frankia bacteria. Availability of optimal Frankia may be a contributing factor in limiting the performance and ecological effects of Alnus, but the factors underlying distribution of Alnus-infective Frankia are not well understood. This study examined the genetic structure (nifD-K spacer RFLP haplotypes) of Frankia assemblages symbiotic with two species of Alnus (A. tenuifolia and A. viridis) in four successional habitats in interior Alaska. We used one habitat in which both hosts occurred to observe differences between host species independent of habitat, and we used replicate sites for each habitat and host to assess the consistency of symbiont structure related to both factors. We also measured leaf N content and specific N-fixation rate (SNF) of nodules ((15)N uptake) to determine whether either covaried with Frankia structure, and whether Frankia genotypes differed in SNF in situ. Frankia structure differed between sympatric hosts and among habitats, particularly for A. tenuifolia, and was largely consistent among replicate sites representing both factors. Leaf N differed between host species and among habitats for both hosts. SNF did not differ among habitats or host species, and little evidence for differences in SNF among Frankia genotypes was found, due largely to high variation in SNF. Consistency of Frankia structure among replicate sites suggests a consistent relationship between both host species and habitat among these sites. Correlations with specific environmental variables and possible underlying mechanisms are discussed.