The Splittail (Pogonichthys macrolepidotus) is a cyprinid endemic to the San Francisco Estuary and its lower watershed. Although it was recently removed from the Federal Endangered Species Act list of threatened species, it is still a species of concern because of uncertainties regarding its abundance and distribution. Because little information is available on early life stages for which to base management decisions, we examined historical long-term monitoring data and conducted a field study in 2002 and 2003 to examine the distribution and habitat associations of age-0 Splittail. During winter and spring, adults migrate from the upper San Francisco Estuary and the Sacramento-San Joaquin Delta upstream into freshwater tributaries and floodplains to spawn. Although previous work suggested a decreasing upstream range for this species, we found that catch data for age-0 Splittail (≤ 50 mm fork length) during a monitoring program spanning 28 years (1976–2003) indicated the upstream-most distribution in the Sacramento River has remained persistent at 232– 296 km upstream from the estuary. Additionally, centers of distribution in the Sacramento and San Joaquin Rivers varied according to hydrology; distance upstream was similar in years of high and intermediate river flows, but increased during low flow years. In all years, age-0 Splittail became abundant in April or May and by June and July had a center of distribution downstream at the margin of the Sacramento-San Joaquin Delta. Our field study showed that in addition to these two primary tributaries, substantial spawning also occurred in other smaller tributaries with previously uncertain importance to Splittail production, namely the Petaluma River, Napa River, and Butte Slough. We also found that age-0 Splittail favor low velocity shallow-water habitats. Compared to main channel habitats, age-0 Splittail were 6.5 times more common in backwaters in upstream riverine locations, and 3.5 times more common in offchannel intertidal habitats in downstream tidal locations. Our study demonstrates the distribution of Splittail is more widespread than previously believed and underscores the importance of offchannel habitats as nursery areas for age-0 fish.