Black core rot is an emerging disease in southern Australian citrus-growing regions that have a Mediterranean-like climate. The major impacts of this disease include pre-harvest fruit drop and unmarketable rotten fruit that can go undetected in the supply chain until it reaches consumers or juicing plants. The disease occurs inconsistently among citrus varieties, growing regions, and seasons, which has resulted in a varied impact across the industry. Alternaria alternata and other Alternaria species have been reported as the causal pathogens of black core rot. A. alternata is also the reported pathogen of Emperor brown spot in humid subtropical and tropical growing regions worldwide, including Queensland. The overall objective of this study is to investigate identities of the Alternaria species associated with black core rot and to better understand their differences to the Emperor brown spot disease. We conducted extensive surveys in citrus orchards in NSW and QLD and obtained a collection of Alternaria isolates from black core rot and Emperor brown spot. Multi-locus phylogenetic analyses placed isolates associated with each disease in the A. alternata and A. arborescens clade, which is polyphyletic and does not resolve the pathogen identities of the two diseases. Reciprocal pathogenicity tests of Alternaria isolates recovered from the two diseases using detached fruit inconsistently produced symptoms among assays, and the difference among the isolate’s pathogenicity requires further investigation. We hypothesise that Alternaria species of the two diseases differ in toxin production. Preliminary mycotoxin analyses suggest that host-specific toxins may not play a role in disease development of black core rot, in contrast to Emperor brown spot. Improved understanding of pathogen identity, pathogenicity and the role of toxins in the black core rot disease cycle may aid the development of a more targeted, cost effective and sustainable integrated disease management program.