This paper discusses three issues that challenge contemporaneous taxonomy, with examples from the fields of mycology and lichenology, formulated as three questions: (1) What is the importance of taxonomy in contemporaneous and future science and society? (2) An increasing methodological gap in alpha taxonomy: challenge or opportunity? (3) The Nagoya Protocol: improvement or impediment to the science of taxonomy? The importance of taxonomy in society is illustrated using the example of popular field guides and digital media, a billion-dollar business, arguing that the desire to name species is an intrinsic feature of the cognitive component of nature connectedness of humans. While continuous societal support of a critical mass of taxonomists is necessary to catalogue all species on Earth, it is shown that this is a finite task, and a proposal is made how a remaining 10 million species can be catalogued within 40 years by 1,000 well-trained and dedicated taxonomists, with an investment of $4 billion, corresponding to 0.0001% of the annual global GDP or 0.005% of annual military expenditures. Notorious undercitation of actually used taxonomic resources and lack of coverage of impact metrics for monographs and other taxonomic work that cannot be published in indexed journals is discussed and suggestions are made how this problem can be remedied. An increasing methodological gap in approaches to taxonomy, between classic morphological and advanced genomic studies, affects in particular taxonomists in biodiversity-rich countries and amateurs, also regarding proper training to apply advanced methods and concepts. To counterbalance this problem, international collaborations bringing different expertise to the table and undertaking mutual capacitation are one successful remedy. Classic taxonomy still works for many groups and is a first approach to catalogue species and establish taxon hypotheses, but ultimately each taxonomic group needs to be studied with the array of methods proper to the group, including descriptive work. Finally, the Convention on Biological Diversity (CBD) and the Nagoya Protocol has put additional burden on basic biodiversity science. Using lichenology in Latin America and Brazil as an example, it is shown that the spirit of non-monetary benefit-sharing proper to taxonomy and systematics, namely capacitation, joint publications, and shared reference collections, has been increasingly implemented long before the CBD and the Nagoya Protocol, and does not need additional “policing”. Indeed, the Nagoya Protocol puts the heaviest burden on taxonomy and researchers cataloguing biodiversity, whereas for the intended target group, namely those seeking revenue gain from nature, the protocol may not actually work effectively. The notion of currently freely accessible digital sequence information (DSI) to become subject to the protocol, even after previous publication, is misguided and conflicts with the guidelines for ethical scientific conduct. Through its implementation of the Nagoya Protocol, Colombia has set a welcome precedence how to exempt taxonomic and systematic research from “access to genetic resources”, and hopefully other biodiversity-rich countries will follow this example.