Greater oil share
Mend has waged a violent campaign against oil facilities in the Delta for more than three years, saying it wants a greater share of oil wealth for its communities.
Mend, represented at the talks by Henry Okah et Farah Dagogo, said in a statement that the two hours of talks were "frank, cordial and useful".
"This meeting heralds the beginning of serious, meaningful dialogue between Mend and the Nigerian government to deal with and resolve root issues that have long been swept under the carpet," the statement read.
Rebel activities have reduced Nigeria's oil output by about a third, from 2.6 million barrels a day in 2006 to about 1.7 million.
In June, Yar'Adua decided to offer an amnesty which led to the surrender of arms by Mend fighters.
Although the group did not take part in the amnesty, it did declare an indefinite ceasefire on October 25 to allow talks to go ahead.