Like other political parties, Kerala Congress also experienced divisions within the party. Various parallel branches have emerged and the irony remains that every faction claims to be the Kerala Congress. Some of the sects of Kerala Congress include- Kerala Congress (Mani), Kerala Congress (Balakrishna Pillai), Kerala Congress (Jacob), and Kerala Congress (Secular). The original Kerala Congress that is recognised officially by the Election Commission of India, is led by P.J. Joseph and it is known as 'Kerala Congress (Joseph)'. The Kerala Congress party is part of the Left Democratic Front.
At the 2001 elections the party won 2 seats in the Kerala Legislative Assembly. KC in the 2004 Lok Sabha polls won the seat of Idukki. After the merger of Kerala Congress with P.C. Thomas's Indian Federal Democratic Party, KC now possesses two seats in the Lok Sabha. Kerala Congress is also part of the ruling United Progressive Alliance. At the 2006 Assembly elections, the Kerala Congress launched 6 candidates of which 4 became successful. As a result, P J Joseph, chairman of the KC(Joseph), was sworn in as the Public Works minister.
By this time, Kerala Congress had also experienced another split as P.C. George formed his own 'Kerala Congress (Secular)'. One of the significant highlights of the party has been to legalise the prohibited business of forest land by the Christian settlers by providing them pattayam.