Geographic variations in sexually selected traits among populations of a species are a potential cause of speciation by pre-mating isolation. A growing number of studies have shown that there is divergence between populations in terms of sound and colour patterns of males, and female preference for male traits. Structure-based ultraviolet (UV) colours have evolved in many animals. Recent studies have suggested that UV colouration may have evolved in response to sexual selection. Specific-specific UV colours may play a role in pre-mating isolation between species. Although some studies have performed on the geographic variations in UV colours and female mate preferences for UV colours, no study has elucidated the proximate causes of producing UV colours among populations. We here report for the first time the nanometer scale structures responsible for producing the geographic variations of UV reflectance in Phintella vittata, a highly iridescent jumping spider (Araneae: salticidae), in which P. vittata males from Yunnan, China have a prominent UV-B peak whereas P. vittata male from Hainan, China have no such a UV-B peak on any body region. TEM observations revealed a four-layer structure in spiders from Yunnan populations and a five-layer structure in spiders from Hainan populations. The distinct UV-B reflection may thus be formed by this kind of structural dimorphism.