Endophytic bacteria from marine macroalgae (EBMM) have aroused interest for their antimicrobial activity, becoming a new source of bioactive compounds for the control of pathogenic bacteria, yeasts and fungi. EBMMs were isolated from Caulerpa sp., Ulva sp., Ahnfeltiopsis sp. and Chondracantus chamissoi collected from Yacila and Cangrejo beach (Piura, Peru). Antimicrobial assays against pathogenic bacteria were evaluated by the cross method, over plate test (OpT) and volatile organic compound test (VOCt). Bacteria with the best antibacterial potential were molecularly characterized, evaluated for antifungal activity and the presence of Iturin, Fengycin and Surfactin genes. Forty-six EBMM were isolated, most of them from the phylum Rhodophyta group and coming from Yacila. In the crossmatch evaluation, 10 EBMMs were found to inhibit gram-positive pathogenic bacteria (Enterococcus faecalis, Staphylococcus epidermidis, Staphylococcus aureus and Listeria monocytogenes) and 12 gram-negative bacteria (Escherichia coli and Salmonella enteric sv typhimurium). These activities were confirmed by OpT and VOCt. The selected strains were identified as 4 Bacillus sp., 2 Kluyvera ascorbata, 1 Pantoea agglomerans, 1 Leclercia adecarboxylata and 1 Enterobacter sp. The strains, P. agglomerans YAFL6, Enterobacter sp. YAFL1, Bacillus sp. YCFR6 and Bacillus sp. YUFE8 showed high antifungal activity on Candida albicans, Candida tropicalis, Colletotrichium sp., Fusarium sp., Fusarium oxysporum and Alternaria sp. In addition, K. ascorbata YAFE21 and Bacillus sp. YCFE4 showed the presence of Iturin and Fengycin genes. The results obtained show the potential of the selected marine bacteria for future applications in the production of antibacterial metabolites and antifungal control.