Mukherjee noted that the bilateral relationship between India and the US has deepened and diversified during Obama's first term and hoped for more progress in the coming years.
"India and the United States share a bilateral partnership which has deepened and intensified in diverse and critical areas of co-operation during your first term in office.
"Ours is a relationship based on shared democratic values of individual liberty, pluralism and respect for the rule of law," Mukherjee said in his message, according to presidential spokesperson Venu Rajamony.
Obama, who travelled to India in November 2010, became the first US President to visit the country in a first term. His re-election as President means he will continue in office till 2016.
"We have built a strategic partnership in areas of shared interest, including matters relating to international peace and security, technological co-operation and in strengthening institutions of global governance. We look forward to the further progress of our co-operation in all these areas during your second term," said Mukherjee.
Obama, 51, defeated his Republican challenger Mitt Romney to win a second term in office.
