This paper studies the evolutionary dynamics of a market regulated by an auctioned emission trading system with a price floor in which there exist three populations of firms that interact strategically: (i) non-polluting, (ii) polluting and compliant, (iii) polluting but non-compliant. Firms that adopt a non-polluting technology need no permits to operate, while firms that use a polluting technology can either buy the required permits (and be compliant) or not (being non-compliant). The latter do not buy emission permits and face the risk to be sanctioned if discovered. From the analysis of the model emerges that all three types of firms coexist at the equilibrium only under specific parameter values. More precisely, it can generically be excluded the coexistence between non-polluting firms and non-compliant polluting ones. The regulatory authority can favor the extinction of non-compliant firms by increasing their probability of being discovered and/or the sanction level. Moreover, the regulatory authority can favor the diffusion of innovation by increasing the permits price floor since polluting-compliant firms exit the market and new non-polluting firms enter the market. However, this policy instrument should be used with caution because it tends to increase also the number of non-compliant firms.