This study presents the second phase of a year-long investigation comparing multiple PCR analyses and histological examinations to confirm the presence of characteristic lesions of each pathogen in three different regions of Latin America. More than 20 agents, including DNA and RNA viruses, bacteria and microsporidia, have been targeted. In addition to wild Penaeus vannamei, which was studied previously, samples of wild P. stylirostris and P. monodon were included. Notably, a positive PCR test result alone does not confirm the presence of a viable pathogen or a disease state. Similarly, positive PCR results do not necessarily correlate with the presence of histological lesions characteristic of the targeted pathogen. Wenzhou shrimp virus 8 (WzSV8) was found to be widespread among shrimp in all regions, including both farm-raised and wild populations. Histopathological analysis indicated that shrimp typically presented coinfections, such as WzSV8, Decapod hepanhamaparvovirus (DHPV), chronic midgut inflammation, and tubule distension/epithelial atrophy, consistent with the toxicity of Pir A/B or another bacterial toxin. Bacterial muscle necrosis was also found in some regions. In general, bacterial infection was the dominant pathology in all three regions during the year. We also postulate that both WzSV8 and DHPV can infect not only hepatopancreatic cells but also cells in the ceca and intestine.