Microbial natural products represent a massive repository of unique chemical scaffolds with corresponding diverse biological functions. However, in the past decade the development of natural products into new therapeutics has dwindled, in part due to the challenges posed by high rediscovery rates and low throughput associated with classical bioassay-guided fractionation methods. Recent research shows that most microbes express only a fraction of their total biosynthetic potential under standard monophyletic culture conditions. The research presented here focuses on applying new cultivation and analytical methodology to marine cyanobacteria and the relatively unexplored microbial communities inhabiting deep sea-hydrothermal vents (DSV). The former group yielded two new antimalarial depsipeptides, companeramides A and B, and two new members of the lyngbyaloside group of glycoside macrolides, with further analogues of each class identified by mass spectral networking of cyanobacterial extracts. A rapid, plate-based fractionation and screening approach was applied to DSV bacteria, along with co-cultivation methodology, to identify new biologically active molecules and the role of these molecules in bacterial interactions was explored by imaging mass spectrometry.