The innovation is the main locomotive of the economic growth and competitiveness. The understanding about innovation process has updated in last decades. The innovation concept not only includes the innovation, but also increases innovation, that can be operated in products but also in the production process, that can be in the conception of the product but also at the level of the market and even at the organizational level. The interactive models of innovation process are put upon linear models and are related with the context, environmental territory. The innovation as a system of innovation became fundamental to competitiveness. Based on these observations, this work intends to analyze the processes and innovation factors, but also enhancing the importance of innovation in system and discussing the main factors which stimulate innovation. The analysis happens on 5 NUTS III at the border of Portugal and Spain. We used the clusters analysis to verify how the companies are positioned in relation to the innovation activities. We intend to characterize the factors and processes of innovation, which distinguish the company’s groupings. The results appear to reveal the existence of three groups of companies and the distinction factors are linked to: general characteristics of companies and its director; initial objectives and innovate sources; cooperation relationships; financial support and obstacles to innovate.Process of Innovation; Regional Innovation Systems; Innovation.