Abstract: The reliable technique for seed and seedling authentic identification is highly desired in forest tree seed and seedling inspection.AFLP(Amplified Fragment Length Polymorphism) is one of the most powerful techniques for this purpose.This paper specially optimized an economic and reliable AFLP analysis protocol for Pinus spp.due to their enormous genome size.The number of selective nucleotides added to the core primers and the primer combinations suitable for AFLP analysis in such species were tested.Some AFLP primer combinations and were screened their utility across different species were tested.The results could also be used as a reference for allowing better amplification in complex templates isolated from plants species with large genomes.