Frequent use of the microbial insecticide, Bacillus thuringiensis kurstaki (Berliner) (Bt), in commercial vegetable greenhouses has led to the evolution of resistance in cabbage looper, Trichoplusia ni (Hübner) (Lepidoptera: Noctuidae), populations. Spatial patterns of Bt resistance suggest that resistant moths disperse from greenhouses selected with Bt to neighboring untreated greenhouses. To quantify dispersal patterns in greenhouse and field populations, molecular markers are desired. We developed a DNA isolation procedure and evaluated the utility of the molecular fingerprinting technique, amplified fragment length polymorphism (AFLP), to analyze the possible population structure of T. ni by using laboratory-reared populations. We also assessed the ability of AFLP markers to distinguish between laboratory and wild T. ni populations collected from a greenhouse and field in the Fraser Valley of British Columbia, Canada. Due to the complexity of the T. ni genome, primer combinations of E 3 and M 4 were required to unambiguously score polymorphic loci. Three of the primer combinations that were examined produced >65 polymorphic bands in laboratory-reared populations, and >90 bands in greenhouse- and field-collected populations. Levels of heterozygosity were higher in wild populations compared with those reared in the laboratory, and AFLP markers reliably distinguished between laboratory and wild populations.