All AOA residencies (i.e. DO residencies) currently will soon be accredited by the ACGME (the body that governs MD residencies). However, the DO residency will need to make sure to meet ACGME requirements before they can truly transition. This transition will be complete by 2020. There are a lot of threads on the subject.
Oh wait, you said merge, not purge. AOA (DO Residency) and ACGME (MD Residency) are fusing to become one type of residency for both MDs and DOs to apply to.