The New York Times has a story describing the fight over the management of New Zealand's hoki stocks.
The New Zealand government has been cutting the allowable catch of hoki by substantial amounts, which indicates that overfishing, predominantly by bottom trawling, has harmed the stock, but hasn't formally admitted that there are problems. From about 275,000 tons in 2000 and 2001 (when the fishery was certified) to about 100,000 tons in 2007 and 2008 — a decline of nearly two-thirds.
Complicating the issue, the fishery is certified by the Marine Stewardship Council, which makes it more popular with buyers. In a subtle way, the MSC label also makes it more difficult for environmental groups to raise objections, as its presence indicating a sustainable fishery, tend to take the wind out of the sails. But the fact that Hoki are caught by bottom trawling, a damaging process that impacts deep ocean benthic systems by dredging up the life on the ocean floor e.g. sponges, corals, while catching both the target species and non-target species. Add to this that the catch limits set by the New Zealand government have caused or exacerbated population declines and it's difficult to see how certification has made the transition to sustainability.
It's lending evidence to the emerging idea that despite the fact that many MSC (or certified) fisheries are well managed and do minimise environmental impacts, the seal alone is not sufficient, to demonstrate a sustainable fisheries. The devil is in the details and consumers need to explore the consequences of their seafood choices.