BRE Properties Inc. has acquired two transit-oriented residential sites on 3.84 acres in the Mission Bay neighborhood of San Francisco for $41.4 million, or approximately $247 per sq. ft. The seller was locally based Focil-Mb LLC.

The two parcels of land, referred to as Blocks 5 and 11, are located along the city’s waterfront and adjacent to the San Francisco Giants’ ballpark. The parcels represented the last two market-rate residential development sites available in Mission Bay.

The San Francisco-based apartment REIT (NYSE: BRE) will develop the entitled sites in phases. The first phase includes 170 market-rate apartment units and 17,000 sq. ft. of retail. The second phase can be developed with an additional 190 market-rate units.

Blocks 5 and 11 are part of the Mission Bay master plan redevelopment, which will include 6,000 residential units, 280,000 sq. ft. of neighborhood retail space, 4.4 million sq. ft. of commercial, medical and biotech lab space, and more than 41 acres of parks and open space.

The Mission Bay neighborhood, which covers 303 acres, represents the largest urban development in San Francisco since the building of Golden Gate Park.

The two parcels acquired by BRE Properties are located near extensive retail and entertainment options, including AT&T Park, the Ferry Building, Union Square and Westfield’s San Francisco City Centre. Access to interstate highways 80 and 280 and U.S. Highway 101 is minutes from the sites.

Mission Bay’s work-life redevelopment plan has attracted a substantial employment base, including the new UCSF Medical Center and research campus, Bayer Healthcare Pharmaceuticals, FibroGen, Nektar Therapeutics, and Old Navy headquarters. Mission Bay also is home to the future 2 million sq. ft. corporate campus of Salesforce.com.

“We are excited about developing two of the last remaining market-rate apartment parcels in the Mission Bay master plan,” said Stephen Dominiak, executive vice president and chief investment officer for BRE Properties, in a press release.

“The lack of available land, strong anticipated revenue growth, limited supply, and proximity to local employers and mass transit will create an ideal environment to support BRE’s future growth in the San Francisco marketplace,” added Dominiak.

BRE Properties expects pre-development work to take place over the next 12 to 15 months, with construction slated to begin in mid-2012.

The REIT owns 75 multifamily communities totaling 21,318 units and has joint-venture interests in another 4,080 units across 13 apartment communities. The apartment complexes are primarily located in major metropolitan markets in Southern and Northern California and Seattle.

Institutional Property Advisors (IPA), a Marcus & Millichap Co. that is a boutique brokerage platform for institutional and private investors, negotiated the sale.

The brokerage team of Stan Jones, Phil Saglimbeni and Sal Saglimbeni represented the seller, Focil-MB.

The stock price of BRE Properties closed Friday at $48.10 per share, up from $39.74 a year ago.