Cyanobacteria and aquatic insects are major components of food webs in freshwater ecosystems. However, the functional relationship between cyanobacteria and aquatic insects has been poorly studied. The blooms of cyanobacteria are more likely to intensify with rising temperatures, such that climate warming may influence this relationship. To improve our understanding of this relationship, we performed a systematic literature review (SLR) and analyzed 104 peer-reviewed research articles published between 1985 and 2020. The articles were categorized into three themes: the role of cyanobacteria as food source and habitat for aquatic insects, the impact of cyanotoxins on aquatic insects, and the use of Bacillus thuringiensis (Bt) expressing transgenic cyanobacteria to control Diptera, mainly mosquitoes. Major findings on each of these themes were summarized and research gaps and opportunities were highlighted. Major gaps include the lack of ecological modelling studies that describe or model this relation, the absence of studies of cyanotoxins' impact on key aquatic insects like dragonflies (Odonata), the impact of Bt larvicidal engineered cyanobacteria on biological indicators like Chironomidae, the lack of studies on climate change impacts on the functional links between cyanobacteria, aquatic insects and other organisms. These gaps and research opportunities should be addressed in future research to increase the understanding of the relationship between cyanobacteria and aquatic insects and therefore the biology of freshwater ecosystems.