For detecting the best gene in phylogenetic and population genetic studies of S. abaster, nucleotide sequences of four mitochondrial genes including Cyt b, 12S and 16S rRNA and D-Loop related to 13 Syngnathus abaster populations in west Mediterranean lagoons were obtained via GenBank and used for analysis. Neutrality tests results significantly were negative for 16S rRNA, 12S rRNA and D-Loop, indicating the effect of recent expansion or directional selection during evolution, whereas the result for MMD analyze wasn’t consistent to the demographic model of sudden expansion. Analyze of molecular variance for each genes show that: the S. abaster populations of west Mediterranean lagoons genetically diverged in three groups including eastern group, western-central group and southern group, as 63-84% of observed diversity belongs to the among groups. Genetic divergence among the central(A2) and western(A1 and A3) populations still wasn’t much and together placed in a common clade(A), whereas divergence levels of eastern and southern populations are very high and each group of populations placed in a separate clade(respectively C and B). Central populations are founder populations which those origins placed in western lagoons in the southern coasts of France and Spain. In addition, a genetic barrier was identified which block the gene flow among eastern and western parts of west Mediterranean lagoons. High divergence among the three clades may be due to geographic discontinuity, habitat conditions such as different temperature, salinity and levels of unsolved oxygen and also effects of evolutionary forces including genetic drift, bottlenecks, natural selection and founder effects. Increasing divergence among three clades during evolution cause creation of subspecies, pripatric speciations and hybrid zone. According to the high levels of genetic diversity and also significant results for phylogenetic, demographic and genetic structure analysis for D-Loop, we can say that this gene is the best one in studies of phylogenetic and genetic structure of S. abaster.