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The potential of digital economy in Indonesia in 2025 is predicted to provide added value up to USD 115 billion. Meanwhile, the adoption of e-commerce by SMEs in Indonesia is still limited. Based on survey of Indonesian E-Commerce Association (IdEA), less than 16 percent of SMEs utilize the marketplace to sale their products. This study aims to analyze factors that influence SMEs in marketing their products through e-commerce. The unit analysis of this study was the SMEs in Yogyakarta. The method of analysis was by using the Importance-Performance Analysis (IPA). By considering internal and external factors that influenced SMEs, It was found that the main factors inhibits SMEs to adopt e-commerce are the lack of knowledge about the marketplace and the ability to look over the market opportunities through digital media. For this reason, It is important to provide business incubator model that is integrated with a training system, mentorship, and access to financing and marketing for SMEs.