Water blooms are a serious environmental problem affecting fresh and marine ecosystem. Application of probiotic bacteria has been introduced as an emerging and eco-friendly tool to regulate or inhibit cyanobacterial blooms. In the present study, we have isolated and identified two different cyanobacterial isolates from El Manzala Lake. Afterward, we examined the anticyanobacterial activity to evaluate their effect on cyanobacterial morphology. Furthermore, the effect on cyanobacterial behavior was evaluated through determination of biomass, reduction percentage of both chlorophyll, phycocyanin using the coculture technique between the selected cyanobacterial isolates and probiotic bacteria (MT2, MT3 and MT4). In this study, the relative high occurrence of cyanobacteria was observed during spring and summer seasons. The isolated cyanobacteria were identified as Trichormus variabilis and Oscillatoriales cyanobacterium. Only, MT2 (Lactobacillius sakei) supernatant displayed anticyanobacterial activity with inhibition zone of 13.6±1.25 and 10±1.44 mm against Trichormus variabilis and Oscillatoriales cyanobacterium, isolated from El-Manzala Lake, respectively. Also, the same supernatant has caused in occurring great morphological changes represented by complete lysis of Trichormus variabilis filaments after 60 minutes. Strong decrease in some photosynthetic parameters in the co-culture between Lb. sakei and each of Trichormus variabilis and Oscillatoriales cyanobacterium, individually, was recorded. For Trichormus variabilis, after five days of incubation, the remarkable reduction percentage of chlorophyll and phycocyanin production was observed and reached 90.85±3.55% and 88.84±3.55%, respectively. In Oscillatoriales cyanobacterium co-culture, the reduction percentage reached 100±0.0 and 91.38±2.99% for chlorophyll and phycocyanin, individually.