Microsatellite markers or simple sequences repeats are DNA - based molecular techniques that are used to see the different among accessions and inbred lines. There are three methods to analysis the results of the polymerase chain reaction of microsatellite markers namely polyacrylamide gel electrophoresis (PAGE), capillary electroforesis, and Metaphor Agarose Gel Electroforesis (MAGE), and the Use of MAGE assessed more easily and economically the polymorphic pattern of DNA markers. This study aimed to obtain fast, effective and efficient in term of easy and cheap technique to identify microsatellite markers of some black rice cultivars and F 2 populations from crosses between black with white rice. The results showed that MAGE successfully separated clearly SSRs alleles with different sizes of less than 25 bp .