Genetic diversity is a fundamental component of biological diversity, and its conservation is considered key to ensure the long-term survival of natural populations and species. National and international legislation increasingly mandates a monitoring of genetic diversity. Examples are the United Nation's Convention on Biological Diversity (CBD) Aichi target 13 and the current post-2020 negotiations to specify a new target for maintaining genetic diversity. To date, only a few pilot projects have been launched that systematically monitor genetic diversity over time in natural populations of a broad variety of wild species. The Swiss Federal Office for the Environment mandated a feasibility study in 2019 for implementing a national monitoring of genetic diversity in natural populations. To obtain information on whether stakeholders are interested in such a systematic monitoring, what they would expect from such a monitoring and where they see respective caveats, we conducted an online survey, which 138 (42% of those surveyed) Swiss stakeholders answered. We find that Swiss stakeholders are generally aware of the lacking evidence regarding the status of genetic diversity in wild populations and species. Accordingly, most stakeholders are interested in a monitoring of genetic diversity and see opportunities for the application of its results in their work. Nevertheless, stakeholders also expressed concerns regarding financial resources and that the results of a genetic diversity monitoring program would not benefit conservation practice. Our findings highlight the importance of stakeholder engagement and demonstrate the value of a detailed stakeholder analysis prior to developing and implementing a genetic diversity monitoring program. A powerful tool for examining the constellation and interactions of the different stakeholders are social network analyses (SNAs). Finally, it is particularly important to communicate transparently about the possibilities and limitations of a genetic diversity monitoring program as well as to closely involve stakeholders from the beginning to increase the acceptance of genetic diversity monitoring and facilitate its implementation.