Stable oxygen- and carbon-isotope profiles from recent specimens of the exotic oyster Crassostrea gigas collected in southern San Francisco Bay were analyzed in conjunction with in situ records of environmental variability to determine the timing of the initial biological invasion and the number of annual cohorts present. Two distinct patterns of isotopic (18O/16O and 13C/12C) variation were identified. The first, found in specimens collected alive from two sites in 2006, is characterized by several unique features that correlate with predicted oxygen-isotope values calculated from temperature and salinity measurements and with records of phytoplankton blooms, indicating that these oysters were recruited at the end of 2001 or early in 2002. The isotope profiles from other specimens differ from these, and do not show evidence of significant environmental events that occurred in 2003, 2004, and 2006, despite the fact that some of these oysters were also collected alive in 2006. These oysters were likely recruited between 1998 and 2000, based on shell growth rates estimated with the von Bertalanffy growth function and on the record of phytoplankton blooms. Poor resolution due to slowed shell growth associated with senescence probably accounts for the absence of the 2003–2006 environmental events in these shell isotope records. These findings indicate that at least two cohorts of C. gigas settled in San Francisco Bay in recent years. That two successful recruitment events occurred over a relatively short time suggests that further recruitment may occur. Such studies as the one conducted here can potentially be used to identify favorable environmental conditions or circumstances associated with past biological invasions as well as those likely to come.