Monitoring for 6 years (2001-2006) showed that the population explosion of the alien ctenophore Mnemiopsis leidyi in the southern Caspian Sea coincided with a decline in the abundance and species number of mesozooplankton. While this decline appeared to have reduced the nourishment of sprat (also known as kilka), it seemed to have affected phytoplankton favorably mainly due to the decrease in grazing pressure. During 2001-2002, when M. leidyi abundance and biomass were at their highest levels, abundance of dinoflagellates and cyanophytes exceeded that of diatoms. Before the invasion (1996) and in some years after the invasion (2003, 2004 and 2006) diatom abundance was higher than the abundance of other groups. In September 2005, an unprecedented bloom of the toxic cyanophyte Nodularia sp. was observed in the southern Caspian Sea. Disappearance of edible zooplankton such as Eurytemora spp. was among the first changes observed after the expansion of M. leidyi in the area. Some changes in the macrobenthic fauna were also conspicuous after the increase of this ctenophore. While the biomass of some deposit feeders, such as the polychaete Nereis diversicolor and oligochaete species increased, benthic crustaceans decreased sharply in abundance during 2001-2003 and completely disappeared during 2004-2006. Iranian catches of kilka, the most abundant and widespread zooplanktivorous fish, decreased significantly in the southern Caspian Sea after 1999. Iranian landings of kilka dropped similar to 70% from 69,070 +/- A 20,270 t during 1995-2000 to 23,430 +/- A 12,240 t during 2001-2006, resulting in a loss of at least 125 million US dollars to the economy. There were also changes in the total catches of large predators such as the kutum and mullet, which mainly feed on kilka, between 1991 and 2006.