The present study aimed to perform molecular identification of lepidopteran larvae from canopy fogging including gut-content analyses. A total of 130 lepidopteran larvae were selected from 37 fogging samples at the Panguana station, district Yuyapichis, province Puerto Inca, department Huánuco, Peru. Target trees were pre-identified and subsequently submitted to molecular confirmation of identity with three markers (rbcL, psbA and trnL-F). The COI gene of 119 lepidopteran larvae was successfully sequenced and found to belong to 92 species: Comparison of DNA barcodes with the reference database of adult moths resulted in 65 (55%) matches at species level, 32 (27%) at genus level, 19 (16%) at subfamily or family level, three just to order level. Three larvae could not be assigned to a family. For these larvae the fogged target tree now suggests a potential host-plant relationship. Molecular gut content analysis, based on High-Throughput-Sequencing was successfully tested for ten larvae corroborating feeding on the target plant in some cases but elucidating several other cases of potential 'alternative feeding'. We propose a larger-scale approach using this rapid and efficient method including molecular gut-content analyses for comprehensively testing the ratio of 'alternative feeders' and pitfalls caused by collateral fogging of larvae from neighboring trees.