Harmful algal bloom (HAB) research and monitoring has traditionally been based on ecological and microbiological measurements which are laborious, time‐consuming, and reliant on experienced operators. Recent developments in oligonucleotide probe technology and immunofluorescence research have revealed several potential applications and techniques that may be transposable to laboratory and field‐based monitoring and research. Field trials are currently underway for fluorescent in situ hybridisation and sandwich hybridisation assays. The former is particularly suited for laboratory‐based research on harmful algal bloom (HAB) population dynamics and structure, whereas the sandwich hybridisation assays based on a portable robotics workstation, offers the potential of quick and reliable laboratory and possibly field‐based screening for HAB species. Initial development is underway for molecular beacons and the Qß replicase detection system, both offer the potential of simple and cost effective strategies for field‐based monitoring by people with minimal knowledge of molecular biology.