The purposes of this study were to validate possibility to using chicken microsatellite marker for investigation of microsatellite variation in Red Jungle fowl genome and used these marker to determine genetic diversity of this chicken ancestor in northern and southern Thailand. Six available microsatellite-flanking PCR primers which developed from genomic libraries of domestic chicken were used to amplify microsatellite DNA from Chelex®100 extracts. Five loci, HUJ1, HUJ2, HUJ7, LEI73 and LEI92 shown polymorphic amplified product (with number of allele at each locus of 9, 12, 8, 10 and 8 respectively) whereas ADL37 shown only two observed allele. Shared allele between northern (Phrae Prayao and Chaiyabhum province) and southern (Chumphon province) local were found at all loci. Conformity with Hardy-Weinberg expectation was found at almost loci (HUJ1, HUJ2, HUJ7 and LEI92) in northern local. Unlike, only HUJ2 and LEI92 loci in southern local conformed this expectation. Geographic heterogeneity analysis shown non-significant difference between two populations at HUJ1 (P = 0.109), HUJ2 (P = 0.313), HUJ7 (P = 0.065) and LEI92 (P = 0.465) but significant difference at LEI73 (P = 0.013).
