Thousands of demonstrators took to the streets of Mukalla, in the southeastern province of Hadramawt, and in Aden, to protest the death of Said Ben Habriche earlier this month.
The local tribal chief was among six tribesmen killed on December 2 in fighting that erupted when his bodyguards refused to hand over their weapons to soldiers at a checkpoint. Two soldiers also died.
The protests were organised by the Hadramawt Alliance of Tribes and the Southern Movement which is seeking a return to independence in the south.
Following the end of British colonial rule in 1967, southern Yemen was independent until union with the north in 1990.
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This was followed by a secession attempt in 1994 that sparked a brief but bloody civil war.
The conflict ended with an occupation of the south by northern forces that laid the ground for many of the disputes over land and jobs that still fan southern resentment.
He told AFP that most shops in Mukalla, the provincial capital of Hadramaut province, were shuttered throughout the day.
A security force said that three southern activists were wounded, two of them seriously, during a firefight with northern street vendors that erupted after activists torched grocery stores.
One of the activists later died of his injuries, said Southern Movement member Fuad Rachidi.
In Aden, the main southern city, thousands of people also took to the streets in support of the Mukalla demonstration and chanted slogans hostile to unity between north and south, an AFP correspondent said.
Later a medical source said a child caught in the crossfire was killed, quoting family members.