<p>Soang gourami fingerling shows variable body sizes eventhough resulted from single spawning. Differences in body sizes among individuals is assumed to be correlated to their genetic component which can be studied using cytochrome b gene PCR-RFLP marker. This study aimed to determine specific PCR-RFLP marker among different sizes of soang gourami collected from single spawning. Genomic DNA was isolated using Chelex method. Cytochrome b gene were amplified and digested using four restriction enzymes. Specific markers were analyzed descriptivelly based on DNA band pattern appear in agarose gel. Ther result showed that PCR-RFLP markers of Cytochrome b-<em>Hinf</em>I of 315bp, and 210bp, and also Cytochrome b-<em>Alu</em>I of 334bp and 189bp are specific markers for large individuals, whereas small individuals are characterized by having Cytochrome b-<em> Hinf</em>I 366bp, and 159bp and Cytochrome b-<em>Alu</em>I 525bp fragments. It is observed that genetic variation of Cytochrome b-<em>Hinf</em>I and -<em>Alu</em>I markers are possitively correlated to body size in soang gourami fingerling. Therefore, both cytochrome b-<em>Hinf</em>I and -<em>Alu</em>I gene can be reffered as specific markers to differentiate among different sizes of soang gourami strain fingerling from single spawning. This result proved that genetic divergences among individuals can be related with certain quantitative characters, such size related. Therefore our study can contribute on fisheries development, especially by providing new technique for fingerling selection to obtain high quality fingerling and also provide new insight the application of molecular technique in fisheries. </p>