Genetic diversity within radiata pine first generation of open-pollinated selections (OPS) from the native resource stands was compared with that observed in native populations to monitor potential changes in genetic diversity during domestication. Genetic diversity was estimated using 58 single nucleotide polymorphisms (SNPs) from 8 expressed genes. Nucleotide diversity maintained in first generation of selections (OPS) (mean π = 0.0036; mean θw= 0.0058) was similar to that found within the native population material (mean π = 0.0043; mean for θw= 0.0065). Likewise, mean values for expected heterozygosity (HE) within and between native population material and OPS were similar (mean = 0.27 ± 0.04) and not significantly different (P = 0.068). Also, the overall distribution of allele frequency classes was not significantly different between native population material and OPS. These results point to no evidence of loss of diversity in OPS due to artificial selection. One possible reason is that the domestication of the OPS is at a very early stage. Another may be that artificial selection in the OPS was based on tree growth and form, not wood properties. The genes selected in this study are mostly involved in cell wall formation, thus genetic diversity of these genes should remain stable between natural population and OPS, unless there was a significant sampling bias in the OPS. Although the SNP information suggests similarities among mainland populations, results from quantitative genetic studies found large provenance differences for growth-, morphological-, stem-form traits, and disease resistance. Determining the threshold at which genetic diversity levels will be significantly reduced during selection should help breeders to make informed decisions regarding the intensity of selection in managed breeding populations as well as gene resource populations.