Populations of sturgeon species have experienced a drastic decline in abundance and distribution in the Caspian Sea basin and are significant conservation species throughout their range. Whereas information relating to the genetic makeup of the population of those species is essential to the development of effective management plans, very little information is currently available. Previous studies have investigated the potential of several types of markers including polyploid microsatellites and mitochondrial DNA markers to provide estimates of population composition. Molecular markers are indispensable and effective tools for studying the genetic structure of populations, phylogeography, gene tags, gene localization, and biodiversity with high levels of reliability, precision and reproducibility. The molecular markers have shown polymorphisms at the DNA level and thus they play an important role in studies of sturgeon biology. According to the results of previous studies, we assume that in sturgeon aquaculture, the selection breeding program using new molecular technologies is an important way to establish a sustainable sturgeon breeding industry in Iran as well as the conservation genetics of sturgeon in the Caspian littoral states. In the present review, we tend to address the applications and success of molecular markers technology in conservation genetics and up to date advancements in the analysis of the genetic structure of populations within the context of fishery management of sturgeon species in the Caspian Sea.