The former Southland chief medical officer, Dr David Tulloch, recently appointed to the DHB-wide role in a restructure, said the marriage was finally being "consummated" .
This meant merging waiting lists, and creating equal access to services throughout Otago and Southland.
Today, the board takes a major step towards a functioning single DHB, when it releases the final shape of merged Dunedin-Invercargill clinical departments.
The board has been consulting on a proposal to create five super departments to replace duplicated structures in the two cities.
The new system meant shared decision-making between clinicians and managers - something firmly in place already in Southland, but a developing concept in Otago, Dr Tulloch said.
At present, different criteria exist for operations in Invercargill and Dunedin, although it varied from specialty to specialty.
Dr Tulloch, a urologist, is stepping down his clinical work to allow him to be almost full-time as CMO, although this has not been immediate because of the DHB's urologist shortage.
Dr Tulloch, an Englishman who as a former Royal Navy doctor served in the Falklands War, and the first Gulf War, admits there is resistance from some doctors.
The DHB is relying on their goodwill to change the ways in which they work - one of the key issues is additional travel.
For doctors employed before the 2010 health merger, which formed the Southern District Health Board, the issue was straightforward, as their contracts took account of the new entity.
Staff employed earlier cannot be compelled to be flexible in terms of travel.
Getting people onside is crucial, and Dr Tulloch is keen for his comments not to seem critical.
Restructuring under way partly resolves the employment issue for those taking new appointments, which would be district-wide. He acknowledged not all the employment issues had been worked through.
"I don't have any illusion that it will be easy," he said.
There is a move, about which Dr Tulloch admitted to being "evangelical", to transferring more procedures and follow-ups to general practice, and trying to better manage chronic conditions in the community.
All of this was hard for clinicians for whom Dunedin Hospital used to be "the centre".
"They have spent all their time looking in. Now they are being asked to look up and out."
For some in Dunedin, it was "a bit of a shock" to discover most of the new executive management team assuming command after a recent restructuring were from the Southland side of the merger.
However, the new team did not see itself as Southland-oriented, and were taking a positive whole-of-DHB approach.
The 58-year-old said his job was not really about daily "firefighting" of hospital-based issues, in which former Otago CMO Dick Bunton would be engaged in a new role.
Dr Tulloch's focus was broader-level oversight, a key part of which was the burgeoning co-operation with other South Island boards in the form of the South Island Health Alliance.
However, one onsite issue he is dealing with is persuading a group of Dunedin Hospital resident medical officers to co-operate in Dunedin Hospital's electronic prescribing rollout.
"The RMOs didn't think their prescribing was bad," Dr Tulloch said.
In a New Zealand first, prescribing would be wholly electronic, rather than written.
Dunedin was "first off the rank" for what would be a nationwide rollout, so it was not surprising it had "created some noise" internally.
The initiative builds on a trial in two Dunedin Hospital wards in 2010, which eliminated some prescribing errors.
Dr Tulloch, who moved to New Zealand from Scotland in 2006 to work in Invercargill, said his new role would see him partly based part time in Dunedin for the first time next month.
