The Glen Ellen Branch's history features unique technology, multiple gauges, and multiple owners. The line was preceded by a prismoidal railroad, using a monorail-like technology that in the latter part of the 19th century was cheaper to construct than a conventional railroad.
The Sonoma Prismoidal Railroad ran for 6 months in the same general corridor of what was to become the Glen Ellen Branch. The ultimate railroad right-of-way was first established by the Sonoma Valley Railroad, which was incorporated in 1878 and built a narrow-gauge line from Sonoma Landing, on San Francisco Bay, to Sonoma. In 1881 the Sonoma and Santa Rosa Railroad extended narrow gauge tracks from Sonoma to Glen Ellen, and was subsequently incorporated into the Sonoma Valley Railroad. This line and its 1888 connection to the San Francisco and North Pacific Railroad between Sears Point and Ignacio were broad-gauged in 1890.
The Glen Ellen branch was effectively a branch line from the Southern Pacific's "interchange" with the NWP at Schellville north to Sonoma and Glen Ellen. These lines were purchased by the San Francisco and North Pacific, and ultimately became part of the Northwestern Pacific Railroad (NWP). The NWP was jointly owned by the Southern Pacific and Santa Fe until 1929, when it became a wholly-owned subsidiary of Southern Pacific. The SP had built its own route into the Valley of the Moon that crossed the NWP Glen Ellen line at Schellville, served Glen Ellen, and continued up the valley to Santa Rosa. In 1934, the SP and NWP consolidated portions of these lines resulting in the NWP between Yulupa and Glen Ellen to be abandoned in favor of the parallel SP line. The Sonoma-Yulupa-Glen Ellen trackage of both NWP and SP were abandoned in 1942. The SP/NWP continued to serve Sonoma until the 1970s.
The portion of the branch to Vineburg, south of Sonoma, shows up on more recent rail maps, but today the track is severed south of Sonoma Airport. Today, in Sonoma at 270 First Street West, a rebuilt railroad depot hosts a local history museum, complete with two vintage freight cars and an SP caboose. (The original depot burned in 1976.) The right-of-way hosts a bike path from this point north. On the east side of town, the tracks have mostly been removed, but are visible in the pavement at Sebastiani Vineyard. The vineyard also has a caboose on site. Railroad crossing pavement markings and embedded rails are still visible on 7th Street, East Napa Drive and along 8th Street to Vineburg. The right-of-way is easily followed paralleling 8th Street from Sonoma to Schellville. At Vineburg, tracks are still in place at a feed mill and extending south about a half mile. They've been torn up from there to just north of Schellville, where a timber trestle still stands and the abandoned tracks wrestle with the roots of a eucalyptus windbreak.
See also the Northwestern Pacific Passenger Station
Also the ICC filings for abandonments on The Santa Rosa Branch and The Wingo-Union Branch.