We employed recently developed statistical methods to explore the epidemic behaviour of hepatitis C subtype 1a and subtype 3a among injecting drug users (IDUs) in Flanders, Belgium, using new gene sequence data sampled among two geographically distinct populations of IDUs. First the extent of hepatitis C transmission across regions/countries was studied through calculation of association indices. It was shown that viral exchange had occurred between both populations in Flanders as well as across international borders. Furthermore, evidence was found suggestive of subtypes 1a and 3a predominantly circulating in subpopulations of Flemish IDUs, exhibiting different degrees of travelling/migration behaviour. Secondly, through coalescent-based analysis the viral epidemic history of the hepatitis C subtype 1a and 3a epidemics was inferred. Evidence was found for different dynamic forces driving both epidemics. Moreover, results suggested that the hepatitis C subtype 3a epidemic has reached a steady state, while the hepatitis C 1a epidemic has not, which therefore might become the predominant subtype among IDUs.