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Much attention is placed on detecting viruses, bacteria and fungi; however, other significant entomopathogens remain overlooked, such as protist and microsporidian parasites. This study employed Nanopore sequencing to explore and phylogenetically analyse microsporidian and protist parasites in reared insects. Using group-specific primers and amplicon pooling strategies, we successfully amplified and sequenced a key protist group (Gregarinasina), microsporidia and fungal pathogens from insect host DNA, providing data for their future detection. Our approach generated novel molecular data, enabling the inference of small subunit and long subunit rRNA phylogenies which enhance the understanding of the evolutionary origin of these parasites. Furthermore, we highlight potential shortcomings of currently available primers and provide new Gregarine-specific primers to aid in further research of these overlooked entomopathogens. 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