Advances in fermentation technology, genetic engineering, and enzyme application technology have increased the use of enzymes. Enzymes can be produced by utilizing a source of microorganisms such as bacteria. Proteolytic bacteria or protease enzyme-producing bacteria are found in foods or plants that contain protein such as the brown seaweed Hydroclathrus sp. This study aimed to obtain protease-producing bacterium associated with marine algae Hydroclathrus sp. from waters around Hoga Island of Wakatobi District and identify the organism based on its 16S rRNA gene sequence. Isolation of bacteria from algae samples was carried out with nNutrient aAgar (NA) media, while proteolytic bacteria selection was carried out on sSkim mMilk aAgar (SMA) media. The bacterial isolates producing proteolytic-clear zone on SMA media were then identified targeting the 16S rRNA gene using the PCR (Polymerase Chain Reaction) method with 27F-1492R primers. Based on the isolation results, there were 3 unique colonies of bacteria that could be cultured from algae samples and coded HIHA-1 to HIHA-3 (HIHA stands for Hoga Island Hydrolathrus macroalgae). The selection process for protease-producing bacteria on SMA media resulted in 1 isolate of proteolytic bacteria, namely HIHA-1. Molecular identification by PCR on HIHA-1 isolate resulted in a single DNA band on the electrophoresis gel sized ~1500 bp. The sequencing results showed a DNA sequence with the size of 1421 bp sharing the highest similarity with the bacterium Exiguobacterium aestuarii strain TF-16 (homology level of 99,93%). In conclusion, the proteolytic bacterial isolate HIHA-1 associated with marine brown algae Hydroclathrus sp. was obtained and identified as Exiguobacterium aestuarii strain HIHA-1.