A new morph of leafy spurge, Euphorbia esula L., was discovered in the floodplains of the Val de Saône (VDS), France. In this region, this emerging weed shows two different morph colours: the common “green” variant and a rarer “red” variant. We compared the sequence data for the plastid trnT–trnF region among individuals of both morphs from the VDS, as well as other populations from Europe and North America, where this plant is invasive. In addition, we analysed the ploidy found among VDS individuals for both colours. Results showed that both morphs share two of the three chloroplast DNA (cpDNA) haplotypes found in the VDS and are both hexaploids (2n=6x = 60). These results suggest that the red morph is only an environmental variant of E. esula subsp. esula. Our results indicate that leafy spurge infestations in this region form a genetically diverse structuring composed of three cpDNA haplotypes, two of which are shared by the two morphs.