One of the problems facing agricultural production in Nigeria is the pests and diseases, which farmers depend heavily on the use of chemicals for their control. However, in time of outbreak of invasive species, difficulties amount on the proper identifications of these species for proper record and management strategies due to reliance on morphological methods of insect identification. The use of morphological methods of insect identification, not only slow but it sometimes leads to variations between experts. The use of Molecular techniques identifies insect species using molecular markers; which minimize false positive results by targeting the specific molecules of interests. This study was conducted to identify major insect pests of crops grown under rotation experiment. Cytochrome oxidase I (CO1) gene was used for the molecular identification of the insect pests of crops under rotation. The expected amplicons were sequenced and the results were analyzed using the nucleotide BLAST at the NCBI database for identification. The COI gene sequences were identified as Pentatomidae sp. BD39 and Mirperus sp. with 97.47% and 99.75% similarities, respectively. The former is a Stink bug and is a pest of cereal grains while the latter is a Pod sucker and is a major pest of cowpea and soybean in sub-Saharan Africa. Taken together, this knowledge is useful in developing different sustainable cropping options in order to monitor different types of insect pests and their population dynamics.