Produk fermentasi tapai singkong madu merupakan produk populer di Indonesia. Terdapat beberapa mikroorganisme yang berperan dalam proses fermentasi tapai singkong madu dan meningkatkan rasa manis yang dimiliki tapai singkong madu. Mikroorganisme genus Aspergillus memiliki banyak peranan dalam proses fermentasi makanan terutama dalam meningkatkan rasa manis dari makanan fermentasi melalui aktivitas enzim amilase. Penelitian terhadap mikroorganisme Aspergillus masih jarang dilakukan dan berbagai analisis yang telah dilakukan pada penelitian sebelumnya seperti analisis morfologi, biokimia, serta analisis molekuler masih memberikan hasil identifikasi yang tidak cukup akurat. Oleh karena itu, diperlukan analisis molekuler lebih lanjut terhadap mikroorganisme Aspergillus sp. TM3 dari tapai singkong madu yang dimiliki oleh Program Studi Biologi Universitas Pelita Harapan untuk dapat memberikan hasil identifikasi yang lebih akurat. Dilakukan pemrosesan data mentah hasil proses sequencing genom keseluruhan Aspergillus sp. TM3 serta dilakukan analisis terhadap tiga gen yang berperan dalam proses identifikasi dalam penelitian ini yaitu gen calmodulin, gen 28S rDNA, dan gen ITS. Proses sequencing terhadap keseluruhan genom Aspergillus sp. TM3 telah memberikan hasil berupa data mentah dalam kualitas baik dan setelah melalui serangkaian proses didapat beberapa fragmen DNA berupa scaffold dengan daerah cakupan sebesar 98,79% dari keseluruhan genom Aspergillus sp. TM3 dan susunan basa nukleotida yang cukup akurat. Sequence gen calmodulin, sequence gen 28S rDNA, serta sequence gen ITS yang dimiliki Aspergillus sp. TM3 memiliki tingkat kemiripan yang tinggi dengan sequence gen calmodulin, sequence gen 28S rDNA, serta sequence gen ITS yang dimiliki Aspergillus welwitschiae dalam database NCBI sehingga dapat dikatakan bahwa Aspergillus sp. TM3 diduga kuat merupakan Aspergillus welwitschiae yang berasal dari tapai singkong madu. / The fermented cassava tapai madu product is a popular product in Indonesia. There are several microorganisms that play a role in the fermentation process of cassava tapai madu and increase the sweetness of cassava tapai madu. Microorganisms of the genus Aspergillus have a lot of roles in the food fermentation process, especially in increasing the sweet taste of fermented foods through the activity of the amylase enzyme. Research on Aspergillus microorganisms still rarely published and various analyzes that have been carried out in previous studies such as morphological, biochemical, and molecular analysis still provide inaccurate identification results. Therefore, further molecular analysis of the Aspergillus sp. TM3 microorganism from cassava tapai madu owned by the Biology Program at Pelita Harapan University is needed to provide more accurate identification results. Raw data processing has been analyzed as a result of the whole Aspergillus sp. TM3 genome sequencing process followed by an analysis of three genes that played a role in the identification process in this study, namely the calmodulin gene, 28S rDNA gene, and ITS gene. The sequencing process of the entire Aspergillus sp. TM3 genome has provided results in the form of good quality raw data and after going through a series of processes, several DNA fragments were obtained in the form of scaffolds with a coverage area of 98.79% of the entire Aspergillus sp. TM3 genome with an accurate arrangement of nucleotide bases. The calmodulin gene sequence, 28S rDNA gene sequence, and Aspergillus sp. TM3 ITS gene sequence have a high level of similarity to the calmodulin gene sequence, 28S rDNA gene sequence, as well as the ITS gene sequence owned by Aspergillus welwitschiae in the NCBI database so it can be concluded that Aspergillus sp. TM3 is strongly suspected to be Aspergillus welwitschiae which comes from cassava tapai madu.