Australia is the largest global producer of pyrethrum, which is grown for the extraction of natural pyrethrin insecticides. Didymella tanaceti and Stagonosporopsis tanaceti are fungal pathogens that pose significant threats to the industry. Although the latter is very well studied, the disease cycle and infection process of D. tanaceti and its interaction with S. tanaceti remains unknown. This study produced five D. tanaceti and four S. tanaceti genetically-modified strains expressing green and red fluorescent proteins, respectively, for the subsequent study of plant-pathogen and inter-pathogen interactions. Agrobacterium-mediated transformation was used to create these strains. Pure cultures of each pathogen were co-cultured with Agrobacterium strains carrying plasmids encoding either mNeonGreen or tdTomato fluorescent proteins. All transformed strains from both species were subject to transformant stability assessment, including confirmation of fluorescence in spores and mycelia, corrected total cell fluorescence (CTCF) of hyphae, growth rate and morphological characteristics compared against non-transformed isolates. Based on CTCF values, strains with varying fluorescence intensities were selected from both species for whole genome sequencing and assembly to characterise the transfer-DNA insertion sites. In both species, transformed strains presented the same morphological features as the non-transformed culture. However, a single transformed strain of D. tanaceti had a slower growth rate than the wild type and was ruled out for future studies. Successfully transformed strains are being used to study the D. tanaceti infection process in pyrethrum, and potential interactions with S. tanaceti in co-infection of living plants.