The environment shapes marine microbial assemblages that impact biogeochemical cycles, but biotic interactions also drive community diversity and metabolisms through the exchange of rare but essential metabolites, such as B-vitamins. Vitamin B12 and vitamin B1 are scarce in ocean, but many microbial planktons including most eukaryotes require them to grow, even if they can’t produce them de-novo (i.e. auxotrophs). However, the seasonality of vitamin auxotrophs and their interplay with the producers on which they depend remain poorly known. Here, we assess the seasonal dynamics of B1 and B12-related prokaryotic communities and their co-occurrence in a Mediterranean coastal site over 7-years. Our metagenomic time series shows a succession of B12 producers with different biosynthesis pathways along the year. Bacteria communities use the aerobic B12 production pathway in summer, and are dominated by HIMB11 and UBA8309, both B1 auxotrophs. In winter, archaea belonging to Nitrosopumilus and Nitrosopelagicus use the anaerobic B12 pathway, and are also able to produce B1 de-novo. Strong co-occurrence patterns between auxotrophs and producers suggest functional complementarity in vitamin requirements between specific microorganisms during vitamin-limited periods. Finally, we show that during environmental perturbations, organisms usually carrying vitamin B12 synthesis genes are replaced by others with the same gene. Such ecological insurance contributes to the long-term functional resilience of marine microbial communities exposed to contrasting inter-annual environmental conditions.