The coexistence principle presents a means for resolving the conflict between prior trademarks and later geographical indications (GIs). This principle has been increasingly adopted in several countries due to recent negotiation efforts of the EU that are meant to combat the ‘first in time, first in right’ (‘FITFIR’) principle promoted by the US. This article focuses on three controversial issues raised in the application of the coexistence principle. The World Trade Organization (WTO) Panel Reports in the Australia-EU (DS290) and US-EU (DS174) disputes related to EU Regulation 2081/92 mentioned these issues but left them unresolved, thereby making space for the EU to require trade partners to widen the scope of coexistence between prior trademarks and later GIs in a manner that runs counter to the WTO Agreement on Trade-Related Aspects of Intellectual Property Rights (TRIPS Agreement). Furthermore, these unresolved issues led to difficulties in applying the coexistence principle and EU-type coexistence clause adopted in non-EU WTO Members. Based on the findings, this article recommends appropriate methods for implementing the coexistence principle that are consistent with the TRIPS Agreement.