A pulmonologist may be the doctor best suited to treat a person with lung disease. Yet a general care physician – looking after the person’s whole-body health – may nonetheless insist that her patient stop smoking.

A similar dynamic applies to West Coast fisheries management. State, regional and federal agencies are specifically charged with regulating fishing, but the marine sanctuaries network has the task of protecting entire marine ecosystems – which inevitably involves fishing. The overlap has generated friction between fishermen and sanctuary managers.

Last fall, under the direction of the 1999 Marine Life Protection Act, the state designated a network of 29 marine protected areas (MPAs) along the Central Coast, 27 within the Monterey Bay National Marine Sanctuary. Roughly 45 square miles of the Sanctuary’s waters are off-limits to fishing.

But while California’s MPAs are limited to state waters, which stretch 3 nautical miles from the coast, the Sanctuary’s 5,300 square miles reach farther offshore into federal waters. In February, after five years of deliberation and roughly 12,000 public comments, Sanctuary Superintendent Paul Michel announced his decision to create MPAs in those federal waters.

A May letter from a fishing group’s attorney attacks Michel’s decision on legal grounds. Creating MPAs usually means limiting fishing, which the Sanctuary has no legal authority to do, according to James Walsh of San Francisco law firm Davis Wright Tremaine. Walsh represents the Alliance of Communities for Sustainable Fisheries, a group of 18 fishing organizations and harbor commissions within Sanctuary waters.

“The Sanctuary’s powers are limited,” Walsh says, citing the agency’s 1992 management plan. “They were never given any authority to regulate fishing; in fact, it was specifically excluded.”

Alliance Co-Chair and Pacific Fishery Management Council member Kathy Fosmark, whose family has been fishing in Moss Landing for four generations, says fishing is already limited in nearly two-thirds of the Sanctuary waters. “There isn’t a need for more MPAs,” she says, “and the Sanctuary doesn’t have the legal authority to do it.”

Only the management council, the state Department of Fish & Game and the National Oceanic and Atmospheric Administration’s fisheries division have the authority to manage fisheries, Fosmark says. In 2002, the agencies closed much of California’s coast to bottom trawling to protect depleted groundfish. In April, the management council voted to close California Chinook salmon fisheries for the 2008 season, due to the low numbers of Sacramento River Chinook spawners.

Fosmark doesn’t see any scientific need to further restrict fishing. “There’s no overfishing going on here,” she says.

Michel counters that federal law directs sanctuary managers to protect and conserve marine ecosystems – which may include limiting fishing in some areas. MPAs are needed to restore ecosystem structure, provide research sites and preserve marine resources in the Sanctuary’s federal waters, he says: “This isn’t about fisheries management. This is about ecosystem management.”

Even so, Michel admits that MPAs typically address the removal of species within their bounds. “It’s a pretty fine line,” he says.

The Sanctuary’s MPA planning process is just beginning, Michel stresses. It will take many years, input from multiple agencies, public input and science to work out the details, including whether and where to restrict fishing.

Walsh, the Alliance’s’ attorney, doesn’t anticipate legal action anytime soon: “My sense is, we’re really just starting this debate.”