The present study was carried out during 2006-2007 along the southern Caspian Sea. The species composition showed that the common kilka, Clupeonella cultriventris caspia, is dominant species with 89% and then anchovy, C. engrauliformis, has shown only 8.7% while it was already dominant species in the past decades. The overall results indicated that common kilka was replaced with anchovy kilka as previous dominant kilka species due to invasion of Mnemiopsis leidyi to the southern Caspian Sea. Anchovy suffered greatly from M. leidyi so that the total catch dropped from 95000 mt in 1999 to less than 20000 mt in 2007. In our survey, 1415 fish specimens were collected randomly, including 221 anchovy, 281 bigeye and 913 common kilka. The mean length of anchovy was 117.8 ± 0.27 mm, while it was about 93.0 mm during 1995 to 1998 before the invasion of M. leidyi. Analysis of age classes indicated the mean age of 4.5 ± 0.04 years for anchovy, 3.6 ± 0.03 for common kilka and 4.6 ± 0.08 for big eye C. grimmi. According to the age and the length structure of the specimens in this study, it could be concluded that in recent years, young fish population of anchovy has been decreased in comparison with the last decade. The results showed that some biological characteristics of kilka population were affected by M. leidyi. Recently fishing activities take place in shallow waters where schools of kilka are in suitable density for fishing. According to our results, ctenophore occupied the anchovy habitat where it was mainly more than 50 m depth. The fishing has moved to areas with depths less than 50 meters where it was the main reason to change in species composition.