Watermelon (Citrullus lanatus) seed meal contains significant amount of extractable protein which can be used as nutritional and functional ingredients in food formulations. Alkali (0.1 M) and NaCl (0.5 M) were used to prepare protein isolates and concentrates from the defatted watermelon seed meals. Protein isolates reported protein yield of 35.15-38.27% and protein content (79.05-83.79%) which was significantly ($p{leq}0.05$) higher than the protein concentrates. SDS-PAGE of protein isolates and concentrates showed major polypeptides in the range of 74.72-110.42 kDa. Also, in vitro pepsin digestibility showed that most of the proteins were readily digested within 30 min of hydrolysis. Amino acids were dominated by arginine, aspartic, and glutamic acid. DSC results indicated that protein concentrates had significantly ($p{leq}0.05$) higher denaturation temperatures than protein isolates. The functional properties of concentrates in terms of solubility and surface properties were better than respective isolates. The results indicated that NaCl extracted proteins had comparatively better functional properties but their yield is significantly lower than respective protein isolates.