Echinococcus multilocularis is the causative agent of alveolar echinococcosis, a severe zoonotic disease. It is maintained through a sylvatic life cycle based on predator-prey interactions mainly between foxes and rodents. Dogs are also good definitive hosts; and due to their close proximity to humans, they may represent a major risk factor for the occurrence of human cases. In two medium-sized cities of Eastern France (Annemasse and Pontarlier), located in highly endemic areas, 817 dog feces samples were collected and analyzed by a flotation technique followed by a multiplex PCR assay. For the first time in France, we assessed the presence of E. multilocularis DNA in four dog feces samples, in which it represents an estimated prevalence of 0.5% (95% CI; 0.1% <> 1.3%). Eight other samples presented taeniid infections from three different species (Taenia crassiceps, Taenia serialis, and Taenia polyacantha). When considering both E. multilocularis and Taenia sensu lato, prevalence rose to 0.6% in Annemasse and 2.6% in Pontarlier. In this highly endemic context, proper application of the usual deworming recommendations (70% of the dogs were treated twice a year or more) failed to prevent dog infection, particularly for hunting dogs. Our results stressed the need to adapt treatment to the environmental context and to the specific activity of dogs. Further epidemiological surveys in domestic dogs and cats using this coprological approach are still needed to obtain a better overview of infection and the associated zoonotic risk.