Agricultural research in the 21st century has become a collaborative effort. Research on crop pests like Spodoptera frugiperda (J.E. Smith), commonly known as the fall armyworm (FAW), can involve international collaboration because it is a pest not only in the southern United States, but also in Latin and South America. Our interest to study the genetic variation of 24 subpopulations of FAW from the southern United States, Mexico, Puerto Rico, Brazil and Argentina required insect collection procedures that preserve the integrity of DNA for molecular genetic analysis. The samples were collected primarily from maize (Zea mays L.), but also included outliers collected from pigweed (Amaranthus sp.), Royal Paulownia (Paulownia tomentosa (Thunb.) Sieb. and Zucc. ex Steud.), lemon tree (Citrus limon (L.) Burm) and Bermuda grass (Cynodon dactylon (L.) Pers.). A common insect preservation technique is to place individual insects in 95% ethanol (ETOH). However, various regulations for shipping and the size of this insect often prevent large sample sizes stored in ETOH from being imported. Genomic DNA from samples preserved in 95% ETOH, lyophilized and fresh insects was extracted and evaluated using DNA quantification and polymerase chain reaction–amplified fragment length polymorphism (PCR–AFLP). All three treatments yielded high-quality/high molecular weight (c. 70–150 μg) DNA. No differences in quality of genomic DNA for AFLP analysis were observed. Lyophilization is a reliable tool to preserve FAW samples, which yields high-quality DNA for use in AFLP genetic analysis.