Marine scientists believe a virulent parasite called MSX is destroying oyster stocks in areas of the Chesapeake Bay that have never been infected by it before, threatening the state's largest water industry.

MSX normally is confined to salty water in the lower bay, but scientists say that with drought conditions the last two years it apparently has worked its way up into oyster-rich areas. In some waters, including the heavily oystered Eastern Bay across the Chesapeake from Annapolis, up to 80 percent of the catch brought up by oystermen is dead, according to Dr. George M. Krantz of the University of Maryland's research center in Crisfield.

The state Department of Natural Resources, which until recently had been witholding judgment on the cause of current unusual oyster mortality, is now reasonably sure MSX is the culprit. "We haven't got it nailed down yet," said Pete Jensen, head of tidewater fisheries for the DNR, "but it looks like MSX. It thrives in the high-salinity, warm-water conditions we've been having the last two years."

There has not been a serious MSX outbreak in Maryland portions of the bay since the 1960s, when areas south of the Choptank River were struck hard by the parasite. That infestation ruined the oyster fishery in affected waters until it abated around 1969 and the oysters gradually came back.

The current mortality, which began last fall but was not attributed to MSX until now, affects waters up to 40 miles north of those hit in the 1960s.

The immediate effect has been a poor oyster year, although that was expected after bad oyster reproduction success in 1975-79. The catch this year is expected to be less than 1.5 million bushels, compared to normal catches well in excess of 2 million bushels. Dockside, oysters bring about $10 a bushel.

What worries oystermen more than this poor year is the prospect of an extended bout with MSX. "The important thing," said Krantz, "is that we can't predict what will happen until we see what the spring floods do. If it's dry and the disease continues, it definitely will have a severe impact" on oystering.

If there's sustained flooding or prolonged high runoff in the spring, which would wash the high salinity out of the upper reaches of the Chesapeake, "it might go away," said Krantz. So far, he added, the MSX has not produced high mortality among small osyters hatched in the last two years, when reproduction was good.

Krantz said worst-hit areas are Eastern Bay, lower portions of the Choptank and Little Choptank Rivers, the Honga River and upper Tangier Sound. Less severely affected are the mouth of the Potomac and the lower Patuxent Rivers.