Here we report the crystal structure of hemagglutinin (HA) from influenza B/HK/8/73 virus determined to 2.8 A. At a sequence identity of approximately 25% to influenza A virus HAs, B/HK HA shares a similar overall structure and domain organization. More than two dozen of amino acid substitutions have been identified on influenza B virus HAs to cause antigenicity alteration in site-specific mutants, monoclonal antibody-escape mutants or field isolates. Mapping these substitutions on the structure of B/HK HA reveals four major epitopes, the 120-loop, 150-loop, 160-loop and 190-helix, that are located close in space to form a large, continuous antigenic site. Moreover, a systematic comparison of known HA structures across the entire influenza virus family reveals evolutionarily conserved ionizable residues at all regions along chain and subunit interface. These ionizable residues are likely the structural basis for the pH-dependence and sensitivity to ionic strength of influenza HA and HEF proteins.