Cystic echinococcosis is one of the most widespread and important helminthic zoonoses, caused by the larval stage of Echinococcus granulosus sensu lato. However, to date there is little information about the disease in West Africa. Faecal and fur samples from 193 dogs, the main final hosts, were collected in 2010 and 2011 in Bamako, Mali. Taeniid eggs were found microscopically in 28/118 (24%) and 80/223 (36%) faecal and fur samples, respectively. One faecal and one fur sample from the same dog were positive for E. granulosus s. l. DNA. In the remaining 27 faecal (96%) and 77 fur samples (96%) only Taenia DNA was detected. Three microscopically positive fur samples were negative by PCR. Sequence analysis of part of the NADH dehydrogenase subunit 1 gene identified the parasite as E. granulosus (genotype G6; Echinococcus canadensis). This is the first study to focus on the final host of E. granulosus s. l. in Mali and the first report of E. canadensis in Mali.