Chloroplast microsatellites represent a new category of molecular markers which can be efficiently used for assessing genetic diversity in forest tree species. Their high degree of polymorphism and their localisation in the chloroplast genome, which is paternally inherited in conifers and therefore do not recombine, allow also the study of evolutionary history of populations. Evolutionary history may have played a more important role than selective processes in determining the present level and distribution of genetic variability, considering the short time span since the last glaciation and the long generation time of conifers of the temperate regions. Using primer pairs flanking simple sequence repeats (SSRs) localised in the chloroplast genome of Pinus thunbergii (Vendramin, et al., 1996, Molecular Ecology 5: 595 – 598), different microsatellites were identified and then sequence characterised in species belonging to the Pinaceae. Chloroplast microsatellite variation within and among populations was analysed in four species, Pinus halepensis Mill., P. leucodermis Ant., Abies alba Mill. and Picea abies K. Sequence data confirmed the high level of conservation of the chloroplast genome. Results indicated the usefulness of this approach for studying history of populations, for monitoring gene flow via pollen, for identifying geographical areas in which most of the variation available today is confined and the origin of populations from different regions. All these aspects assume high relevance in population and conservation genetics and in particular the information which can be obtained by the use of this approach is extremely valuable to set guidelines for the conservation of the genetic resources and for the establishment of genetic reserves. Keywords: haplotypic diversity, evolutionary history, Pinus halepensis Mill., Pinus leucodermis Ant., Abies alba Mill., Picea abies K., Polymerase Chain Reaction, chloroplast microsatellites
