Unravelling the relationship between biological diversity and ecosystem resilience is a timeless topic dating back to Alexander von Humboldt’s expeditions in the early 19th century. While global oceanographic expeditions and basin-wide transects show positive correlations between microbial diversity and temperature or productivity, they often lack temporal replication, and include few high latitude observations especially during winter months. Here, using seasonal amplicon sequence data from six time-series in the northern and southern hemispheres, we show that on a multiannual basis marine microbial alpha-diversity (species richness and evenness) correlate most strongly with day length, rather than with temperature and chlorophyll a (as proxy for primary production), independent of the targeted 16S rRNA hypervariable region. By integrating data from 2003 to 2020, our evidence suggests that microbial diversity and annually recurring community composition are governed by similar principles, from subtropic to polar oceans. These global trends are consistent regardless of the collection methods, DNA extraction chemistry, sequencing technologies or bioinformatic pipelines. Hence, to understand drivers of marine microbial diversity, larger-scale studies need to embed their analyses into the context of regional seasonal variations. Overall, our synthesis reframes the fundamental drivers of marine microbial diversity as phenological, and suggests that although the state of the temperature and chlorophyll spectra should be considered, it is regular sampling over seasonal cycles that can disentangle these effects. Our findings support the idea that microbial diversity patterns and ecosystem stability are regulated by holistic feedback systems. Or as Alexander von Humboldt already stated, Nature is interconnected, linking ‘the little things’ with global interactions and patterns will allow us to place the observed microbial diversity into the bigger picture.