Before being used as raw material for chocolate production, cacao beans subjected to a fermentation process. The most important part of the fermentation process is microbes and enzymes that play a role in the fermentation process in this case are pectinase enzymes. The presence of pectinase enzyme is very important in the cocoa bean fermentation process, due to pectinase plays a role in the degradation of pectin contained in the pulp, which generate faster fermentation process. In this study, out of 137 isolates (yeast and bacteria) were screened as pectinolytic producer and found 4 isolates as a pectinolytic producer from bacteria, namely IDI-001, IDI-002, IDI-004 and IDI-008. However, none of yeast to produce pectinolytic. Isolate IDI-001 has the highest clear zone and pectinolytic activity with 1.06 mm and 1.80 U mL−1, respectively, followed by IDI-002, IDI-004, and IDI-008 with clear zone diameter and enzyme activity 1.00 nm, 0.84 nm, and 0.81 mm and 0.95 U mL−1, 0.62 U −1 mL, and 0.43 U mL−1, respectively. Based on 16S rRNA identification, isolate IDI-001 has 100% similarity to Bacillus subtilis. Characterization of pectinase activity has shown that Bacillus subtilis IDI-001 produced pectinase enzyme with higher activity 1.80 U mL−1 at 48 h and pH 7.0. Further investigations are needed to characterize the pectinase enzyme and its ability to cacao beans fermentation process.