Detection of infectious hypodermal and hematopoietic necrosis virus (IHHNV) in shrimp aquaculture is complicated by endogenous viral elements (EVEs) causing false positives in conventional PCR assays. This study analyzed 277 Penaeus vannamei samples from Ecuador using World Organization for Animal Health (WOAH)-recommended shortfragment primers (IHHNV-309, -389, -392, -77012; ~1.5 kb amplicons) and long-amplicon PCR (LA-PCR; ~3.7 kb, 90% of the genome), complemented by histopathology.