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Introgression frequently occurs between closely related plant species when there is incomplete reproductive isolation. However, few studies have been designed to examine the extent and direction of introgression from all three genomes, especially when they have different rates of gene flow. Conifers, in which chloroplast (cp), mitochondrial (mt) and nuclear (nr) genomes show contrasting rates of gene flow, provide a good model in which to carry out such a case study. Here we use data on sequence variation in 18 DNAs from three genomes for 311 individuals of 31 populations to investigate the extent and direction of introgressions between three spruce species in areas where they are sympatrically distributed. We found that one species seem to have introgressions derived from the other two species in areas of sympatric distribution; there were more introgressions from the maternally inherited mtDNA, which has the lowest rate of gene flow, and fewer introgressions from the bi-parentally inherited nrDNA. Further coalescent analysis of nrDNA population genetic data suggested that the species containing introgressions had experienced range expansion in the recent past while there was no such indication for the other two species. Our results support the hypotheses that introgressions occurred more frequently at genetic markers with lower rates of gene flow and that they usually took place from local species towards invading species that had undergone recent demographic expansion. [ABSTRACT FROM AUTHOR]