Molecular cytogenetics has led to major advances in understanding how angiosperm plant genomes are organized and evolve. In the past several years, the use of cytogenetics in the analysis of gymnosperm genomes has gained credibility with the demonstration of fluorescent in situ hybridization using ribosomal RNA gene probes in a number of conifer species. The physical mapping of the 18S-26S ribosomal DNA and the 5S ribosomal DNA in white spruce and a related western North American species, Sitka spruce (both 2n=24), provided sufficient chromosome markers to reliably karyotype each species. Despite overall karyotype similarities, interspecific differences in the genomic distribution of the ribosomal DNAs and a 138 bp white spruce satellite DNA were observed on five of the twelve chromosome pairs and may be useful markers to investigate the natural hybridization of these two spruces in British Columbia. Progress in generating additional cytogenetic markers in white spruce and Sitka spruce, and in lodgepole pine, will also be presented. Lastly, in order to fully integrate cytogenetic approaches in studies of conifer genome organization and evolution, research avenues which are likely to allow the routine detection of single copy sequences on conifer chromosomes will be discussed.