Establishment of nonindigenous species (NIS) has emerged as one of the leading environmental problems in the Great Lakes basin over the past quarter century. The purpose of this study was to assess responses by government agencies regarding allocation of funding to NIS projects between 2000 through 2005. NIS is considered a major and increasing problem by eight of ten major funding agencies in the basin. Despite this, total funding decreased from $5.1 to $3.2 million dollars per annum and the number of projects supported declined concomitantly from 145 to 98 during this period. Control or ecosystem effects received the greatest allotment of resources and represented the largest number of projects. Non-taxonomic specific topics, including risk assessment and ballast tank assessment and management, received more funding than any taxon-specific projects and comprised the majority of studies on prevention, spread, and socioeconomic impacts of NIS. Among the latter, fish and Dreissena mussels were the most popularly funded topics, and comprised the largest contribution to ecosystem effects and biology studies. Control studies principally addressed sea lamprey, round gobies and carp species. Prevention studies had the highest funding rate per capita ($ per study). Surprisingly, no clear shifts occurred with respect to the relative importance of projects pertaining to prevention over the period studied despite the recognized importance of this aspect of research.