Obama also won the Democratic contest in the western state of Wyoming over the weekend, although the sparsely populated state had only a few delegates.
Key contest ahead
The Mississippi primary is the last to be held before the important contest in the eastern state of Pennsylvania, which holds 158 delegates, in April.
The state's Gulf coast was badly hit by Hurricane Katrina in 2005 and both Democratic candidates have outlined proposals to rebuild local communities devastated by the disaster.
Although Republicans are also holding a primary, John McCain, the Arizona senator, clinched enough votes last week to win the party's presidential nomination.
The Mississippi vote comes as Democratic party leaders discuss whether to repeat primary contests in the states of Florida and Michigan, which were both stripped of their delegates after moving their primaries to earlier in the year.
However both states say a repeat of the vote could prove expensive, with proposals to hold a mail vote in Florida alone possibly costing up to six million dollars, local politicians said.
On Monday Obama also criticised remarks from the Clinton team that proposed the possibility of a joint Obama-Clinton campaign, with Obama as the vice-president.
"With all due respect ... I don't know how somebody who is in second place is offering the vice presidency to the person who is in first place," Obama said on Monday while campaigning in Mississippi.
Obama currently holds has 1,579 delegates while Clinton, senator for New York, has 1,473, according to the latest AP tally.
Either candidate must win 2,025 delegates to clinch the nomination, however the contest could go on to the Democratic party's convention in August.