Infectious hypodermal and haematopoietic necrosis virus (IHHNV) was first noted in blue shrimp Litopenaeus stylirostris (Stimpson) in mid-1981. Since that time, at least 12 species of penaeoid shrimp have been reported to be infected with IHHNV. Pacific white shrimp Litopenaeus vannamei (Boone) represents a shrimp species highly refractory to the disease, whereas L. stylirostris was highly susceptible to the disease. Since the beginning of the shrimp farming industry in Ecuador, viral diseases have been observed in L. vannamei and L. stylirostris. Of these, L. vannamei represents approximately 80% of cultured shrimp. Histopathology, ultrastructure and in situ DNA hybridization confirm the presence and assess the prevalence of IHHNV in pond-reared shrimp, and especially in abnormally small animals of both species. Although IHHNV may be considered enzootic in cultured L. vannamei in Ecuador, we did not find high prevalence (Cowdry A bodies) in specimens of diseased pond shrimp before 1996. From that time to 1998, a higher prevalence of IHHNV has been observed in both species. The epizootic of the IHHNV disease has been related to the oceanographic and climatological conditions caused by El Nino. In addition, it has been suggested that large quantities of wild shrimp post-larvae of both species that were stocked in shrimp farms, infected as latent carriers in 1997, from which the virus could spread to a larger population of these shrimp in 1998.