Captive-breeding programs and reintroduction initiatives are increasingly implemented to combat population declines and extirpations. In implementing a captive breeding program, a number of decisions are made, including the source of the broodstock and mate pairing system. Captive-breeding programs are also known to induce selective pressures; therefore it is critical to evaluate whether conservation goals are being met. Here, we evaluate the progress of a captive breeding program for a threatened salmonid in the San Joaquin River in the Central Valley, California, USA. Spring-run Chinook salmon were extirpated from the upper San Joaquin River following the construction of the Friant Dam in 1942. A captive-breeding program was established in 2012, in an effort to reestablish spring-run Chinook salmon in the San Joaquin River using fish from extant populations in the Central Valley. Each year, eggs are subsampled from crosses performed at the nearby Feather River Hatchery. Through an analysis of ~ 10 years of genetic monitoring and phenotypic data, we asked whether the program has minimized inbreeding and selective pressures induced by captive breeding. Phenotypic data included traits of the adult broodstock (e.g. age-at-maturity, body size) and early-life history survival of captive progeny. We found that the breeding program has adequately captured the genetic diversity of the source population and that mate pairings guided by kin relatedness reduced inbreeding. We also found that traits of the female parent influenced the survival of their offspring; survival of captive progeny was lower when female parents were older or when egg size was smaller. More broadly, these findings provide a case study for how to evaluate the success of captive-breeding programs given the challenges associated with conserving small populations.