Abstract: Molecular studies using Random Amplified Polymorphic DNA profiling was carried out on some moss species from Ile-Ife, Nigeria in order to determine their genetic variation and species relationships. The result obtained revealed that the chloroplast DNA isolated using the SDS method produced higher yields though lesser quality, while those isolated using the Kit method produced lesser yield but higher quality. All the seven primers employed in this study showed RAPD fragments with varying bands ranging from 200 Bp to 3000 Bp. Out of a total of 55 individual fragments obtained from the seven primers used, 27 bands were polymorphic while 28 were species specific (unique).