The Vancouver-based company says in a statement that the guards were shot at their guard post early Wednesday (Philippine time).
Both guards worked for a security contractor and the deaths are under investigation by Philippine National Police.
These deaths follow the shooting death of a long-time employee last December at the same operation about 350 kilometres south of Manila.
B2Gold said that incident involved an altercation between employee Jessie Villegas and a security guard who was later arrested by police.
The mining and milling operation on the island of Masbate was acquired by B2Gold through a merger with CGA Mining Ltd., that was completed in early 2013.
B2Gold's other mining operations are in Nicaragua and Namibia and it has properties in Mali, Burkina Faso and Colombia.