SECLUDED among loam hills in central Queens, before the advent of urban zoning and brick row houses, sprawled a storied peat bog known locally as Juniper Swamp. The bog, used in the 1920's by the gangster Arnold Rothstein as the site of a phantom village built to dupe potential property buyers, earned a niche in the archives of quirky city history.

In the early 1900's, however, what most intrigued nearby residents was Juniper Swamp's astonishing diversity of plant life. Describing the place in The Journal of the American Peat Society in 1918, a botanist named Roland M. Harper marveled that the bog's ''vegetation is different from any other bog known to the writer.''

Mr. Harper noted the presence of leatherleaf, a shrub with gold-dotted leaves, and the herb arrowhead, neither of which is found anywhere else in the five boroughs. What particularly piqued his interest, and what made Juniper Swamp a destination for picnickers, was the abundance of blueberry bushes. But as Mr. Harper predicted, noting encroaching development by a railroad, among other projects, ''This unique bog is doomed.'' He was right. The fabled bog and the unusual plants that thrived in it were converted into Juniper Valley Park and housing lots in Middle Village, and retired to the musty cellars of local memory.

The history of New York's flora is rich and kaleidoscopic, fraught with conflict and struggle. Over the years, the city has been home to a remarkable range of plants, exotic and ordinary, invasive and innocuous. Now, drawing inspiration from the conservation-minded botanists who chronicled the city's flora in the late 1800's and early 1900's, a team of taxonomists, researchers and volunteers at the Brooklyn Botanic Garden are documenting all the plant life within a 50-mile radius of Central Park. The effort, known as the New York Metropolitan Flora Project, is the first systematic attempt to record the metropolitan region's plant life in nearly a century. A major goal of the study, which began in 1990 and is expected to last 10 more years, is to identify species that have declined or disappeared. A lot has changed since the last survey in 1915.

''Many species have been lost,'' said Gerry Moore, a botanist with the Brooklyn Botanic Garden. ''Many species are barely hanging on in parks where they used to be fairly common.''

Mr. Moore and his colleagues estimate that about a third of the plants native to the five boroughs have disappeared in the last 100 years. Part of that decrease is attributable to what Steven Clemants, the botanic garden's vice president for science and the flora project's founder, called the ''bull's-eye effect.''

''Where the dense urbanization occurs,'' Dr. Clemants said, ''plant species are being lost.'' He noted that some species once common to the city, like blueberries, rhododendrons and mountain laurel, have declined but continue to thrive in the suburbs. Pollution, road salting and competition from nonnative plants like the Oriental bittersweet have also contributed to the decline or disappearance of species.

Occasionally, as in the case of the American bittersweet, a native vine with brilliant red-orange fruits, the reasons for a plant's dwindling numbers in the city might be more elusive. ''One reason they think American bittersweet has declined is that people were over-collecting it for Christmas decorations,'' said Steven Glenn, the flora project's chief field researcher.

Like Juniper Swamp and its blueberry bushes, the tale of the city's fleeting flora is inextricably bound in with the history of its vanishing natural habitats. On the hallowed ground where Yankee Stadium now stands, there was once an expansive marsh known as Jerome Avenue Swamp that was home to many notable plants. Among them were the spreading globe flower, a rare buttercup that may have disappeared from the city.

In the late 1800's, botanists collected terrestrial orchids from a tidal marsh along the Brooklyn-Queens border on the rim of Jamaica Bay. Today, 25 species of orchids native to the city, including the yellow lady-slipper, spotted coralroot and dragon's mouth, are in decline or gone completely.

Eric Lamont, a research associate with the New York Botanical Garden and the president of the prestigious Torrey Botanical Society has published several papers on the city's orchids. While native orchids have all but disappeared, Dr. Lamont and others have documented an attractive, cream-colored orchid originally from Europe that is blooming throughout Brooklyn and Queens. ''It grows like a weed,'' Dr. Lamont said, his voice tinged with admiration, not contempt.

The city's plucky foreign orchid, the helleborine, grows out of sidewalk cracks, by roadsides, in cemeteries. It has also has done well in one specific location. ''This nonnative orchid is growing all over Ellis Island,'' Dr. Lamont said.

Two other city natives — swamp pink, a lily boasting bright pink flowers, and the Sea Beach amaranth, a low-growing coastal plant — may also soon be gone. Both are on the federal endangered list.

The tree of heaven, or ailanthus, made famous by Betty Smith's novel ''A Tree Grows in Brooklyn'' and believed a few years ago to be threatened by a fungus, has defiantly clung to life. It even made a recent flora project list of the 50 most prevalent woody plants in the metropolitan region. The project's scientists have seen the tenacious, gangly, junkyard dog of a tree leaning out of second-story windows of abandoned buildings, pushing its leaves up through subway grates from underground.

''I have a real respect and awe for it,'' Mr. Glenn said of the tree. ''There's a couple in my backyard. My old superintendent hacked one really severely one summer. He took every limb off. The thing came back vigorously and grew 20 feet next summer.

''It almost mocks any attempts to get rid of it,'' he added. ''It's almost saying, 'Is that the best you got?' ''

Drawings: Some 25 species of orchids native to the city, including the yellow lady-slipper (right), the spotted coralroot (far right) and the dragon's mouth (below left), are in decline. They are crowded out by nonnatives like the Oriental bittersweet (below right). (Illustrations by Dolores R. Santoliquido; right, Emma Skurnick/Brooklyn Botanic Garden)

Adam Fifield is the author of the memoir ''A Blessing Over Ashes: The Remarkable Odyssey of My Unlikely Brother'' (Morrow).