White cypress pine (Callitris glaucophylla) is a drought-tolerant evergreen conifer, which is a member of the Australian C. columellaris species complex. The complex is comprised of five closely related morphospecies that occur in a wide range of bioclimatic regions in Australia. Ecological genomics of the complex provides an opportunity to identify markers associated with environmental adaptation and is expected to broaden our understanding of its speciation process. We adopted a single-tree linkage mapping approach combined with high-throughput restriction site associated DNA (RAD) sequencing and expressed sequence tag-simple sequence repeat (EST-SSR) genotyping to set up a baseline genetic map for C. glaucophylla. The generated linkage map consisted of 4284 markers positioned on 11 linkage groups, corresponding to the haploid chromosome number of Callitris (2n= 22). The spatial distribution of markers was uneven compared to random expectation with significant clustering in central positions of some linkage groups, which may be associated with recombination cold spots of pericentromere regions. Allelic segregation was shown to be distorted in particular regions of four linkage groups, where selection may have operated on viability genes, leaving allelic distortion in surrounding linked markers. We then tested RAD single nucleotide polymorphisms (RAD-SNP) marker recovery and transferability of the linkage map to population genomic data collected for a related species, Callitris gracilis. Of the linkage map markers, 1257 markers (ca. 30 %) were recovered in independent RAD sequencing of population samples of C. glaucophylla. Genetic diversity and differentiation evaluated using mapped markers reflected ascertainment bias slightly; a decrease in Hs (absolute difference of -0.018) for a related species (C. gracilis) and an increase in F-ST between C. glaucophylla and C. gracilis (+0.018) were detected. Although care should be taken given such biases in cross-species transfer, this study demonstrated that the RAD-SNP-based linkage map is essentially useful when combined with population genomic analysis of this conifer lineage.