Two different strategies to amplify anonymous fragments from the genome of Maltese Goat were studied. The first strategy ultised "arms" generated by restriction digests of amplicons. Ligation of the "arms" to a fragment from the goat genome were amplified using the primers complimentary to "arms", by a standard PCR technique. The second strategy involved the utilisation of arbitrary primed PCR known as Random Amplification of Polymorphic DNA (RAPD) and utilised a single 10 bp primer. A total of 66 Maltese goats were studied using the RAPD methods and 11 polymorphic zones were identified. The proportional incidence of presence and Polymorphism Information Content (PIC) of these zones were calculated. Due to the fact that in RAPD PCR only a single primer is used, these zones could not be sequenced directly and thus were cloned in a pUC 18 vector. Eleven different clones were sequenced using both the forward (universal) and reverse primers specific for the pUC 18 vector. After sequencing a total of nine new markers for the goat genome were identified and their homologies with known nucleic acid and protein databases were described.