The aim of this study was to identify Saprolegnia spp. isolated from inffected common carp Cyprinus carpio L. eggs and fry in two fish hatcheries (Al-Manahel and Al-Wahda) in the middle part of Iraq, during the period from March-June 2009. It was evident from molecular diagnosis (PCR Technique) that isolates of the genus Saprolegnia, shared one feature (production of secondary zoospores with long hooked hairs). These isolates were divided into four groups based on the findings of molecular diagnostics PCR. Isolates of Saprolegnia spp. were characterized genetically and physiologically. The majority (25 from45) of the isolates in both hatcheries were almost genetically identical as assessed by RAPD-PCR. The remaining isolates belonged to three different groups.