Maccullochella is a genus of large predatory fish commonly known as cods native to the Murray-Darling Basin and some coastal drainages in eastern Australia. Of the four recognised species of Maccullochella, three are of high conservation concern. Furthermore, trout cod (M. macquariensis) exhibit substantial male bias in collections of broodstock, indicating that sex-specific processes may be at work limiting recruitment, survival, and population resilience. Alternatively, trout cod may have a sex determination mechanism that does not result in a 50:50 ratio of females:males. Karyotyping suggests a heterogametic (i.e., XY) sex determination system in Maccullochella that would produce a 50:50 sex ratio. However, identification of genetic variants useful for genetic sex determination has been challenging. Genetic markers that can genetically sex Maccullochella would improve the understanding of population dynamics and how sex-specific demographic processes may limit populations of these species. Such markers are very useful in conservation or directed breeding programs to support sex-specific husbandry and target sex ratios among other benefits. Genetic sex determination is one trait that can be better understood through the assembly of reference genomes, and may rely on large structural variants such as X and Y chromosomes in vertebrates. Sex determination in vertebrates may also be controlled by master sex genes such as sdY in salmonids or be under polygenic control. We generate new, high-quality genomes of three species of Maccullochella: Mary River cod (M. mariensis), eastern freshwater cod (M. ikei) and trout cod to at first, investigate genetic sex determination in Maccullochella. In addition to the immediate application to investigation of sex determination, the reference genomes will provide other benefits to the broader Maccullochella scientific community.