Nutritional co-dependence (syntrophy) is observed in natural microbial communities and has underexplored potential to improve biotechnological processes by using cooperating cell types. So far, design of yeast syntrophic communities has required extensive genetic manipulation, as the co-inoculation of most eukaryotic microbial auxotrophs does not result in cooperative growth. Here we employ high throughput phenotypic screening to systematically test pairwise combinations of auxotrophic S. cerevisiae deletion mutants from a genome-scale knock-out library. While most auxotrophic co-culture pairs indeed do not enter syntrophic growth, we identify 49 auxotroph pairs which defy the general rule and spontaneously form syntrophic, synergistic communities. We then characterise the stability of nine selected co-cultures and show that initial inoculation ratios of co-cultured populations significantly influence growth dynamics. We demonstrate that a pair of tryptophan auxotrophs grow by exchanging a pathway intermediate rather than the end product indicating that the metabolic space for metabolic interactions is larger than currently assumed. Exploiting this observation, we introduced a malonic semialdehyde biosynthesis pathway split between different pairs of auxotrophs, including the tryptophan auxotrophs, and obtained a 6-fold increase in relative production titer of a biotechnologically relevant compound. Our results report the spontaneous formation of stable syntrophy in a specific subset of S. cerevisiae auxotrophs and illustrate the biotechnological potential of dividing labour between a naturally cooperating intraspecies community.