One of the components to control the international trade with endangered species of fauna and flora is the European Community border security. Because the trade of wild animals and plants crosses borders between countries, the effort to regulate it requires international cooperation to safeguard certain species from overexploitation. The CITES was conceived in the spirit of such cooperation. All import, export, re-export and introduction from the sea of species covered by the Convention has to be authorized through a licensing system. Each Party to the Convention must designate one or more Management Authorities in charge of administering that licensing system and one or more Scientific Authorities to advise them on the effects of trade on the status of the species. Implementing the CITES, the relevant European Community regulations and directives related to endangered wild animals and plants in international trade of the Republic of Lithuania, customs has become one of the main institutions to control the trade. For the global legal means to restrict the endangered species of wild animals and plants, their parts and products of their trade, import and export, the article examines the implementation of the customs activity of the CITES convention. Customs, while implementing endangered animal and plant protection, controls how to keep determined prohibitions, restrictions and special requirements. Efficiency of security depends on the cooperation of surveillance authorities and customs. International trade regulation methods are mainly associated with certain additional or specific requirements, e.g., a license, permit, certificate, conformity declaration and the like.This article analyzes the problems occurring at customs by implementing the CITES convention.