Blood samples were collected to determine genetic markers associated with twinning in the Egyptian Al-Barqi, Al-Baladi and Al-Zaribi goat breeds. Animals were selected from experimental stations of the Animal Production Research Institute using pedigree records. Both Al-Zaraibi and Al-Baladi are among the most productive breeds of Egyptian goats, and each of them has been divided into a prolific and non-prolific group. DNA extraction process from blood samples was handled by two molecular fingerprinting techniques. Random polymorphic DNA (RAPD) molecular markers were used to characterize the three breeds. Micro-satellites, or simple sequence repeats (SSRs), were used to detect genetic polymorphisms within each of the prolific and non-prolific groups. The DNA micro satellites used are: ILST019, INRA0005, MAF0065, SRCRSP0005, SRCRSP0024, McM0527 and OarFCB0020. For constructing a combined Dendrogram dealing with genetic relationships among the three goat breeds studied, the data generated from molecular markers were introduced to SPSS package programme according to binary values (1,0); Bands were scored as 1 if present or 0 if absent. The output results involved both different hierarchical pair-wise distances (UPGMA) and constructed dendrogram .The RAPDPCR analysis indicated that each goat population had unique banding patterns. On the other hand, the RAPD-PCR analysis of amplified DNA samples showed that it can differentiate between prolific and non-prolific breeds of goats. The selected micro satellite markers showed little informational abilities about prolific and non-productive females with the exception of INRA0005 and OarFCB0020. INRA0005 was the most polymorphic and therefore the most informative.