Recent investigations have established core principles by which septins can form non-polar filaments in vitro. How cells then assemble, regulate and use septin polymers is still only beginning to be understood. It is clear that there is plasticity and variability in septin organization across diverse species and cell types. Work in the filamentous fungi has been invaluable in discovering this variation in form and function. In particular filamentous fungi display many forms of higher order septin structures and study of septins in these systems has led to insights into septin assembly, dynamics and regulation. Importantly in many cases work in these alternative systems reveal differences to how septins may be organized, functioning or regulated in Saccharomyces cerevisiae. Here I review the novel aspects of septin biology found in filamentous fungi and raise many open questions about these enigmatic polymers that should guide future study.