Recent advances in genome complexity reduction and sequencing make possible the genome-wide analysis and identification of genes under natural selection. We applied DNA sequence-capture to the analysis of two conifer species, Pinus taeda and Pinus eliottii, that are widely distributed in the south-southeastern US. Haploid DNA from megagametophytes was extracted from seeds of 24 trees of each species, collected from native populations in 11 states (AL, AR, FL, GA, LA, MD, MS, NC, SC, TX and VA), that represent the natural range of the species. For genotyping, libraries were prepared by sequence-capture of a small portion (0.03%) of the Pinus genome that represents 14,729 genes. Six multiplexed pools, of eight barcoded DNA samples each, were hybridized to sequence-capture oligonucleotides and sequenced in a high-throughput sequencer (Illumina’s HiSeq). Interspecific and intraspecific SNPs are currently being identified from the sequence data. The data will be used to establish a detailed view of linkage disequilibrium in genic regions of the loblolly and slash pine genomes. The availability of data from both species will also allow the analysis of the relationship between within-species diversity and between-species divergence, which has not yet been possible at this scale.