Location of family Satellite DNA (HindIII SatDNA) on chromosomes of Acipenser persicus and Acipenser gueldenstaedtii was analyzed using Fluorescent in Situ Hybridization (FISH) technique to determine the genetic differences between these two species. After obtaining suitable metaphase plates using leukocyte culture and HindIII SatDNA extraction from genome of the fish under study, extracted SatDNA from genome of A. gueldenstaedtii was used as a FISH probe. The probe was labeled with spectrum orange (Orange-dUTP) and hybridized with chromosomes of the fish under study. Analysis of SatDNA sequences isolated from A. persicus and A. gueldenstaedtii showed the presence of 163bp for A. persicus and 168bp for A. gueldenstaedtii. In the study of metaphase plates 66±4 signals were detected from the hybridization of the probe used with chromosomes of A. persicus and 68±3 signals were detected from the hybridization of the probe with chromosomes of A. gueldenstaedtii. Due to presence of numerous microchromosomes and heterogenous and large hybridization signals, it was impossible to identify the precise position of signals on chromosomes. The following results are worth mentioning: 1. developing leukocyte culture method for A. gueldenstaedtii and completing it for all of the Caspian Sea sturgeons. 2. Developing a suitable culture medium for the Caspian Sea sturgeons. 3. Isolating sturgeons HindIII Satellite DNA family from A. persicus and A. gueldenstaedtii, determining sequences and registering the sequences in the NCBI gene bank (FJ429174; FJ 94465). 4. Developing a protocol for FISH technique in A. persicus and A. gueldenstaedtii which has opened a new era in aquaculture genetic studies entitled Molecular cytogenetics in the country. Considering its potential applications, this technique can be applied to other aquatic species.