Official figures reported to the agency showed that the DRC had 12 cases and six deaths while Guinea had 18 cases and nine deaths, according to the update.
Seven healthcare workers are amongst the confirmed cases, two in DRC and five in Guinea.
The Africa CDC, in its Ebola virus cross-border updates, indicated that between February 15 to March 12, some 18 Ebola virus-related alerts were reported in Sierra Leone.
It, however, stressed that all alerts were investigated and tested negative for Ebola virus, as it emphasized that there are no confirmed Ebola cases from Sierra Leone so far.
Meanwhile, the agency called on all African countries to enhance their cross-border surveillance efforts by mapping population movements to identify all potential crossing points where there is risk of disease spread.
African countries have been urged to set up screening posts and conduct health screenings for travellers with signs of Ebola, as well as implement public health measures at border crossing points including temperature monitoring, and infection prevention and control measures.
It also called on AU members continue performing contact tracing and follow up of all probable and confirmed cases, as well as enhance infection prevention and control measures in health care settings, health care workers protection and practice safe and dignified burial.
New outbreaks of the deadly Ebola virus disease in the two African countries are sending new jitters to Africa as the continent is still grappling with the Covid-19 pandemic.
The 2014-2016 West Africa Ebola virus outbreak claimed over 11,300 lives, with over 28,600 recorded cases.
Ebola is a highly contagious hemorrhagic fever that causes a range of symptoms including fever, vomiting, diarrhoea, generalized pain or malaise and in many cases internal and external bleeding.