This work describes the mycelial fungal diversity associated with leatherback sea turtle nests and eggs from Mayagüez-Añasco Bay Coast (MABC), Puerto Rico. Comparisons are made of conditions previous to leatherback nesting season, during leatherback nesting season, and during nest hatching season. Prior to Dermochelys coriacea nesting season, the fungal community along the MABC showed a normal distribution (p = 0.098) by One-Way ANOVA. We found that Aspergillus was the most frequent genus (0.15), followed by Cladosporium (0.09) and Curvularia (0.08). At the time of oviposition, Penicillium was the most frequent isolate (0.15), followed by Cladosporium (0.11), Aspergillus (0.11), and Fusarium (0.07). No fungi were isolated from nesting leatherback's ovipositor samples. During hatching season, fungal diversity was evaluated from the sand of hatched nests and from failed eggs. Fusarium solani was the most frequent isolate (0.57) from hatched nest sand and was the only species isolated from the interior of failed eggs. A strong positive correlation was obtained between fungal abundance and the number of failed eggs in the nests (r = 0.853, p < 0.001). This was the first attempt to study fungal diversity associated with D. coriacea nests and eggs in Puerto Rico.