Sesame (Sesamum indicum L.) is one of the oldest oilseed crops, primarily grown in the tropical and subtropical regions of Asia, Africa, and South America. It is a valuable source of oil, protein, calcium, and phosphorus. In the 1990s, there was an unsuccessful attempt to establish a sesame industry in Australia. However, in 2018, efforts were renewed to establish the industry by introducing high-yielding, non-shattering sesame varieties that can be harvested mechanically. Unfortunately, sesame crops are affected by various disease-causing fungi, which can lead to significant production losses, particularly during post-harvest and storage phases. These seedborne fungi can damage seed quality and germination, resulting in poor growth of infected seedlings and an increased risk of pre-emergence and post-emergence diseases. The current investigation aims to identify the seedborne fungi associated with harvested sesame seeds. Seed samples were collected based on factors such as site, year of planting, season of planting, and seed coat color, and then seeded on agar plates to allow for fungal growth. The different seedborne fungi were identified through sequencing of the Internal Transcribed Spacer (ITS) region. Differences in the detected seedborne fungi and their prevalence were observed based on the site, year of planting, season, and seed coat colour. This information will be valuable in developing strategies to prevent the spread of sesame diseases and manage these seedborne fungi, thereby minimizing crop yield losses.