This study was conducted to provide sustainable measures for conservation and management to protect valuable natural/ecological resources, offer differentiated quality assurance services for eco-tourism products, and explore measures for eco-tourism certification/designation systems. To achieve its goals, the study discussed domestic and overseas trends and literatures that concern eco-tourism certification/designation system and investigated case studies that were presently operational. A group of experts and a group of non-experts were surveyed separatedly to investigate the awareness of the national eco-tourism certification/designation system. The results from the investigation indicate that Europe, since the late 1990s to early 2000, has actively introduced a system that establishes and operates a dedicated institution, and European members have created a cooperation framework to formulate international partnerships and develop standardized assessment benchmarks to adhere to the goals of the system, the period for certification was designated from one year to five years, and renewals were granted based on periodic monitoring and reassessment. In Korea, from early 2000, the Ministry of Culture, Sorts and Tourism and other organizations have certified product quality and assessed travel products and national park tour programs. The certification period was established to be set between one and three years, and the vast majority were not reassessed. Upon investigating the results for awareness of national eco-tourism certification/designation system, a high number of respondents agreed with the need to establish a eco-tourism certification/designation system (90% of respondents), and the respondents cited eco-tourism quality assurance, conservation of value, means to maintain established institutions, and environmental education and information as reasons for needing a certification/designation system. In Korea, a certification/designation system for the eco-tourism industry is presently in operation, but the system regulates target institutions based on their characteristics. Therefore, this study proposes its suggestions via various categories, including designated institutions, designated purpose, designated subjects, designated organization, laws, regulations, and incentives.