This study investigates the impact of four different ocean analyses on coupled forecasts of the 2006 El Niño event. Forecasts initialized in June 2006 using ocean analyses from an assimilation that uses flow-dependent background error covariances are compared with those using static error covariances that are not flow dependent. The flow-dependent error covariances reflect the error structures related to the background ENSO instability and are generated by the coupled breeding method. The ocean analyses used in this study result from the assimilation of temperature and salinity, with the salinity data available from Argo floats. Of the analyses, the one using information from the coupled bred vector (BV) replicates the observed equatorial long wave propagation best and exhibits more warming features leading to the 2006 El Niño event. The forecasts initialized from the BV-based analysis agree best with the observations in terms of the growth of the warm anomaly through two warming phases. This better performance is related to the impact of the salinity analysis on the state evolution in the equatorial thermocline. The early warming is traced back to salinity differences in the upper ocean of the equatorial central Pacific, while the second warming, corresponding to the mature phase, is associated with the effect of the salinity assimilation on the depth of the thermocline in the western equatorial Pacific. The series of forecast experiments conducted here show that the structure of the salinity in the initial conditions is important to the forecasts of the extension of the warm pool and the evolution of the 2006 El Niño event.