Transposable element (TE) display is a sensitive and efficient experimental method to detect TE insertions. It is a modified form of Amplified Fragment Length Polymorphism (AFLP), the difference being that one primer is designed according to a TE sequence in TE display. Here we report the development of TE display using a short interspersed nuclear element (Sine200) in the African malaria mosquito, Anopheles gambiae. We have shown that Sine200 display is highly specific and reproducible and we were able to recover and sequence multiple Sine200 display bands to identify specific insertion sites. Relatively high levels of insertion polymorphism were observed between seven A. gambiae field populations. A random survey of 18 insertion sites revealed significant genetic distance between the M and S forms of A. gambiae, some of which are sympatric populations. However, TE insertion frequencies at these loci are similar between populations within each form. In addition, we have developed a locus-specific PCR assay to use polymorphic Sine200 insertions as co-dominant genetic markers. Both TE-display and locus-specific PCR results are consistent with the hypothesis that the M and S forms of A. gambiae may be two incipient species.