Hatching failure is one of the threats to the declining sea turtle population. Sea turtle egg fusariosis, an emerging fungal disease, has been linked to lower hatching success in sea turtle nests. The disease is associated with the presence of members of the (Fusarium solani species complex (FSSC). Samples of cloacal mucus, nest sand, eggshells, and eggs were collected from seven hawksbill turtles and their corresponding nests at Melaka’s nesting beaches and hatchery site. FSSC was prevalent in the unhatched eggs (n = 32) from the seven study nests, colonising 96.9%. The remaining eggs from the study nests were found to have high hatching success, with a mean of 85.8 ± 10.5% (n = 7). It is unknown if the presence of FSSC contributed directly to embryonic mortality in this study. There are two possible roles of FSSC in sea turtle eggs: as a saprophyte or a primary pathogen. The presence of FSSC in the nest did not always compromise the hatching success of the entire egg clutch. FSSC was not detected in the sand samples of all nests, even though all nests contained Fusarium-colonised eggs. The concentration of FSSC in the sand might influence the infection rate of sea turtle eggs and their hatching success. Best practices for hatchery must be in place to achieve high hatching success for sea turtle conservation.