Insect movement in the landscape remains often poorly known and in some cases does not make it possible to understand the role of the different cultivated and wild habitats in the dynamics of useful and pest insects. Insects are among the greatest pests of agriculture, horticulture and forestry worldwide, inflicting damage and economic costs both directly and by transmitting plant viruses. There is a need for tracking the migrant insects in agroecosystems through space and time to establish their migration. Furthermore, tracing the origin of pest insects allows to design more rapid, efficient and environment-friendly control systems (less use of insecticides). Tracking insects can also help us better understanding their biology (e.g. insect population dynamics, geo-traceability, feeding behavior and other ecological interactions). However, tracking insects presents a considerable challenge as they are often small, cryptic and highly mobile organisms. The most common methods of analysis currently proposed (microsatellite markers, stable isotopes) do not allow for the moment to determine their geographical origin. The ecological niche occupied by the insects highly influences the bacterial communities associated with the insects. Hence understanding the diversity of bacterial communities could be an option to trace the orgins of the pest. This paper presents two new protocols used to extract bacterial DNA from the Cotton Bollworm, Helicoverpa armigera and the analysis of this DNA by PCR-DGGE. This promising method is proposed as a new traceability tool which provides insects with a unique biological barcode and makes it possible to trace back the insects to their original location.