This study evaluated the toxicological and antibacterial activity of crude extract of endophytic bacteria’s protein associated with the red algae Eucheuma spinosum which was produced at various incubation times. The external and internal proteins of the potential bacteria were collected on the incubation times which were 18, 24, 30, 36, 42, 48, and 54 hours. The evaluation toxicological of protein used Brine Shrimp Lethality Test (BSLT) method and the antibacterial activity of protein towards E. coli and S. aureus were measured using the diffusion method. Seven bacteria were successful to be isolated from these algae (ES01, ES11, ES21, ES22, ES23, ES24, and ES25), the Isolate ES25 was a genus of Vibrio and its protein had the potential to be produced. External protein levels were higher than internal, so it continued with the next phase. The extracted protein of (PE42) was active towards S. aureus (12.0 mm) while the extracted protein of (PE36) is active toward E. coli (9.0 mm) and also highly toxic to the larvae of Artemia salina Leach (1.596 μg/mL). The external protein of endophytic bacteria ES25 (Vibrio) associated with red alga Eucheuma spinosum was potentially produced in the time of incubation above 36 hours to get the highest toxicity and active antibacterial.