Pineapple cultivation is of economic importance for farmers; however, pineapple production can be affected by pests and diseases. Recently, the presence of mealybugs and pineapple mealybug wilt-associated viruses (PMWaV)-1, -2, and -3 has been reported in the provinces of Satipo and Chanchamayo, in Peru’s central jungle. This study aimed to molecularly identify mealybugs collected from the Hawaiiana cultivar and the MD-2 hybrid in those provinces to determine if they are indeed hosts of the PMWaV-1, -2, and -3. Through amplification and sequencing of the internal transcribed spacer ribosomal genes, the mealybugs were identified as Dysmicoccus brevipes. In the phylogenetic analysis of these D. brevipes, Peruvian isolates were associated with isolates from India, China, Taiwan, and Japan. In addition, our results confirmed the presence of PMWaV-1, -2, and -3 in all mealybug specimens collected from both the Hawaiiana cultivar and the MD-2 hybrid tested, with these PMWaVs showing a 99% sequence identity with others recently reported in Peru. Therefore, D. brevipes is a host and probable vector of PMWaV-1, -2, and -3 for the cultivar Hawaiiana and the hybrid pineapple MD-2 in Satipo and Chanchamayo, Peru. Based on these findings and observations of crop management strategies in these provinces, we recommend integrated management practices to control this pest.