The first time the white spot disease (WSD) and IHHNV were reported in Iran was in 2004 and 2008, respectively in Bushehr Province. In Sistan and Balochestan province only the WSD was reported in 2008.The aim of this study was detecting these two viral diseases in these provinces, during December 2009 to April 2010. A total of 364 samples were collected according to suspected gross signs from hatcheries and shrimp farms in Bushehr and Sistan and Blochestan provinces (I.R. Iran) respectively, including larvae (72, 43 samples), post larvae (48, 37 samples), juveniles (57, 32 samples), sub adults (39, 22 samples) and broodstock (29, 13 samples) of Litopenaus vannamei . WSD was detected from juveniles (23 samples), sub adults (14 samples), and broodstock (14 samples), and IHHNV was also detected from juveniles (16 samples), sub adults (9 samples) and broodstock (5 samples) based on gross signs, PCR and histopathological changes from Bushehr province but from Sistan and Blochestan province only WSD was detected from juveniles (26 samples), sub adults (18 samples) and broodstock (7 samples). Histopathological observations of WSSV showed basophilic Cowdry type A inclusion bodies in all tissues such as gills, haematopoietic tissue, cuticle epithelium, lymphoid organ and connective tissue. However histologically, the hepatopancreas tissue showed vacuolization of B cells , without inclusion bodies, but histopatholgical changes caused IHHNV including eosinophilic Cowdry type A inclusion bodies which were ectodermal, mesodermal and rarely endodermal.