Election officials launched the review of nine percent of votes from the July 2 election at polling districts in 26 of Mexico's 32 states under the supervision of 192 judges and representatives of political parties.
Officials have set a Sunday deadline to complete the recount, and until August 31 to resolve all pending questions. A president-elect must be named by September 6 and assume office on December 1.
Based on initial results, conservative National Action Party (PAN) candidate Felipe Calderon won by a mere 0.58 percent of the vote.
But his opponent, Lopez Obrador, has refused to concede defeat and alleged the election was marked by widespread fraud.
Leading a campaign of street demonstrations and acts of civil disobedience, Lopez Obrador and his Party of the Democratic Revolution (PRD) have demanded a full recount of all 41.7 million votes cast.
But Mexico's electoral tribunal on Saturday rejected Mr Obrador's recount petition, instead ruling for the partial recount at polling stations where it believed there were possible irregularities.
The tribunal's decision disappointed Lopez Obrador's backers, who say they will continue their protest campaign demanding a complete recount.
Most of the polling districts affected by the recount were won by Mr Calderon based on initial results but PRD leaders say there were irregularities in how ballots were tallied.
As the recount got underway, supporters of Mr Obrador blocked the offices of three foreign banks in the latest protest against alleged electoral fraud.