A climatology of the thermodynamic phase of the clouds over the Southern Ocean (40–65°S,100–160°E) has been constructed with the A-Train merged data product DARDAR-MASK for the four-year period 2006–2009 during Austral winter and summer. Low-elevation clouds with little seasonal cycle dominate this climatology, with the cloud tops commonly found at heights less than 1 km. Such clouds are problematic for the DARDAR-MASK in that the Cloud Profiling Radar (CPR) of CloudSat is unable to distinguish returns from the lowest four bins (heights up to 720–960 m), and the CALIOP lidar of CALIPSO may suffer from heavy extinction. The CPR is further limited for all of the low-altitude clouds (tops below 3 km) as they are predominantly in the temperature range from 0°C to −20°C, where understanding the CPR reflectivity becomes difficult due to the unknown thermodynamic phase. These shortcomings are seen to flow through to the merged CloudSat-CALIPSO product. A cloud top phase climatology comparison has been made between CALIPSO, the DARDAR-MASK and MODIS. All three products highlight the extensive presence of supercooled liquid water over the Southern Ocean, particularly during summer. The DARDAR-MASK recorded substantially more ice at cloud tops as well as mixed-phase in the low-elevation cloud tops in comparison to CALIPSO and MODIS. Below the cloud top through the body of the cloud, the DARDAR-MASK finds ice to be dominant at heights greater than 1 km, especially once the lidar signal is attenuated. The limitations demonstrated in this study highlight the continuing challenge that remains in better defining the energy and water budget over the Southern Ocean.