Abstract. An ocean data assimilation system to assimilate Argo temperature (T) and salinity (S) profiles into the HYbrid Coordinate Ocean Model (HYCOM) was constructed, implemented and evaluated for the first time in the Atlantic Ocean (78° S to 50° N and 98° W to 20° E). The system is based on the ensemble optimal interpolation (EnOI) algorithm proposed by Xie and Zhu (2010), especially made to deal with the hybrid nature of the HYCOM vertical coordinate system with multiple steps. The Argo T–S profiles were projected to the model vertical space to create pseudo-observed layer thicknesses (Δ p_obs), which correspond to the model target densities. The first step was to assimilate Δ p_obs considering the sub-state vector composed by the model layer thickness (Δ p) and the baroclinic velocity components. After that, T and S were assimilated separately. Finally, T was diagnosed below the mixed layer to preserve the density of the model isopycnal layers. Five experiments were performed from 1 January 2010 to 31 December 2012: a control run without assimilation, and four assimilation runs considering the different vertical localizations of T, S and Δ p. The assimilation experiments were able to significantly improve the thermohaline structure produced by the control run. They reduced the root mean square deviation (RMSD) of T and S calculated with respect to Argo independent data in 34 and 44%, respectively, in comparison to the control run. In some regions, such as the western North Atlantic, substantial corrections in the 20 °C isotherm depth and the upper ocean heat content towards climatological states were achieved. The runs with a vertical localization of Δ p showed positive impacts in the correction of the thermohaline structure and reduced the RMSD of T (S) from 0.993 °C (0.149 psu) to 0.905 °C (0.138 psu) for the whole domain with respect to the other assimilation runs.