In response to the threat of introductions of non-native forest insects, the Early Detection and Rapid Response (EDRR) program in Alaska monitors for arrivals of non-native insects, an effort that is limited by the time required to process samples using morphological methods. We compared conventional methods of processing EDRR traps with metabarcoding methods for processing the same samples. We deployed Lindgren funnel traps at three points of entry in Alaska using standard EDRR methods and the trap samples were later processed using routine sorting and identification based on morphology. The samples were then processed using High Throughput Sequencing (HTS) metabarcoding methods. In three samples bycatch was included and in three samples non-native species were added. This dataset includes all of the raw FASTQ files obtained from HTS sequencing. Complete specimen and occurrence data are available via an Arctos (https://arctosdb.org/) archive at https://arctos.database.museum/archive/2017_edrr_ngs_test_records. Sequence data have been deposited in in the NCBI Sequence Read Archive under BioProject PRJNA542936. Complete sample data are provided in the file 2017_EDRR_STDP_sample_data.csv.