This study reported the application of a next generation sequencing (NGS) analysis of yeast diversity in native Indonesian fruit, Durio kutejensis, collected from Borneo, Central Kalimantan. The analysis was designed to observe the microbial consortium associated with solid state fermentation (SSF) for amylase production. Together with the additional data from culture-dependent analysis, we observed the morphological features, molecular characteristics, and amylase concentration produced by each isolate. We performed Solid State Fermentation (SSF) for amylase production and the enzyme activity was then determined using UV-Vis spectrophotometer at 540 nm. Result obtained from metagenomic approach consist of 4 group that fungal species included in the Ascomycota identified as Botryosphaeria dothidea (1.35%), Lasiodiplodia crassispora (17.62%), Aureobasidium pullulans (55.02%), Paraphoma chrysanthemicola (11.38%), Preussia funiculate (1.90%), Sporormiella intermedia (0.82%), Myrothecium gramineum (1.35%), Fusarium oxysporum (6.24%), Fusarium proliferatum (3.25%) and Phialemoniopsis curvata (1.08%). The results of isolation using culturable medium in the form of YMA obtained 40 yeast isolates. A total of 40 representative isolates from durian fruit were screened, two positive amylase isolates based on clear zones formed were DU 4.2 (Candida sorboxylosa) and DU4.22 (Cyberlindnera fabianii) isolates with amylolytic index of DU 4.2 isolates at 0.24 and DU 4.22 at 0.72 with an incubation time of 48 h. The highest amylase enzyme activity was found in isolate DU 4.2 of 31.21 U / mL.