Non-random association of alleles in the nucleus and cytoplasmic organelles, or cyto-nuclear linkage disequilibrium (LD), is both an important component of a number of evolutionary processes and a statistical indicator of others. The evolutionary significance of cyto-nuclear LD will depend on both its magnitude and how stable those associations are through time. Here, we use a longitudinal population genetic data set to explore the magnitude and temporal dynamics of cyto-nuclear disequilibria through time. We genotyped 135 and 170 individuals from 16 and 17 patches of the plant species Silene latifolia in Southwestern VA, sampled in 1993 and 2008, respectively. Individuals were genotyped at 14 highly polymorphic microsatellite markers and a single-nucleotide polymorphism (SNP) in the mitochondrial gene, atp1. Normalized LD (D 0 ) between nuclear and cytoplasmic loci varied considerably depending on which nuclear locus was considered (ranging from 0.005-0.632). Four of the 14 cyto-nuclear associations showed a statistically significant shift over approximately seven generations. However, the overall magnitude of this disequilibrium was largely stable over time. The observed origin and stability of cyto-nuclear LD is most likely caused by the slow admixture between anciently diverged lineages within the species' newly invaded range, and the local spatial structure and metapopulation dynamics that are known to structure genetic variation in this system. Heredity Keywords: cyto-nuclear; linkage disequilibrium; metapopulations; spatiotemporal; Silene Keywords: cyto-nuclear; linkage disequilibrium; metapopulations; spatiotemporal; Silene INTRODUCTION Population genetic studies generally focus on either the nuclear or the cytoplasmic (mitochondria or chloroplast) genome. Additional insights can be gained by measuring joint allelic associations at loci derived from nuclear and cytoplasmic genomes, or cyto-nuclear linkage disequilibrium (LD). Analyses of cyto-nuclear LD can document evolutionary and demographic trends in population genetics. Processes like structure (Nei and Li, 1973), gene flow (Asmussen and Schnabel, 1991) and non-random mating/inbreeding (Asmussen et al., 1989;Slatkin, 2008) all influence cyto-nuclear LD. Selection-based treatments of cyto-nuclear LD focus on the importance of epistatic interactions between the nuclear and cytoplasmic genomes (Wade and Goodnight, 2006;Brandvain and Wade, 2009). Theoretical investigations of genetic drift predict an influence of population size on the variance of LD measurements (Datta et al., 1996). Additionally, demographic processes have been shown to greatly facilitate non-random associations between the nucleus and a cytoplasmic genome. For example, cyto-nuclear LD (or lack thereof) is an informative metric when considering admixture of two populations of the same species (Arnold, 2006). Thus, cytonuclear LD will be driven by the interaction of spatiotemporal selective and demographic parameters specific to a system of study, or by non-equilibrium population dynam...