Monitoring of Genetic Variation of Allozyme Analysis. Konferensi Akuakultur Indonesia 2013. Biochemical genetic markers have been increasingly used for inferences on the population genetic structure of marine fish. The research aimed to determine the genetic variation on milkfish from different locations with allozyme analysis. Samples were collected from 4 different locations i.e, Aceh, Bali, Gorontalo and Halmahera. Results showed that number of allele per locus and polymorphic loci were ranged 1.6-1.9 and 60-70%, while heterozygosity was ranged from 0.199-0.307. The highest heterozygosities was observed from Bali Population. Milkfish populations from Halmahera and Gorontalo have closest genetic distance of 0.0324, while Aceh and Gorontalo population has the farthest genetic distance of 0.1733. Bali population had better genotype compared to milkfish from other regions.