The present study has the following aims; first, to examine the evolution of microsatellite loci both among and within pine species by sequencing alleles both among species and within populations (I, III). The persistence of microsatellites was studied among pine species with very different effective population sizes (I). Second, we used microsatellite markers together with other molecular markers and an adaptive trait (date of bud set) to study patterns of genetic variation in Scots pine (Pinus sylvestris) in Finland. We wanted to solve if patterns of variation are comparable between molecular markers and quantitative traits (II). Third, we evaluated the usefulness of microsatellites in population studies. We examined the distribution of genetic variation in five natural populations of radiata pine (Pinus radiata). We were able to compare our results to the earlier results based on allozymes. In addition, we examined whether the population size reductions in the past have an effect on the allele frequency distributions. Genetic distance methods based on both IAM and SMM were compared (III). Finally, we used microsatellite markers and a newly developed Bayesian method to estimate the inbreeding coefficients of individual adult trees from natural populations of radiata pine in the presence of null alleles and PCR amplification failures (IV).