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Somali National Movement, Barre persecution

The moral authority of Barre's government was gradually eroded, as many Somalis became disillusioned with life under military rule. By the mid-1980s, resistance movements supported by Ethiopia's communist Derg administration had sprung up across the country, which led to the Somaliland War of Independence. Barre responded by ordering punitive measures against those he perceived as locally supporting the guerrillas, especially in the northern regions. The clampdown included bombing of cities, with the northwestern administrative centre of Hargeisa, a Somali National Movement (SNM) stronghold, among the targeted areas in 1988. The bombardment was led by General Mohammed Said Hersi Morgan, Barre's son-in-law.

In May 1988, the SNM launched a major offensive on the cities of Hargeisa and Burao, then the second and third largest cities of Somalia. The SNM captured Burao on 27 May within two hours, while the SNM entered Hargeisa on 29 May, overrunning most of the city apart from its airport by 1 June.

According to Abou Jeng and other scholars, the Barre regime rule was marked by a targeted brutal persecution of the Isaaq clan. Mohamed Haji Ingiriis and Chris Mullin state that the clampdown by the Barre regime against the Hargeisa-based Somali National Movement targeted the Isaaq clan, to which most members of the SNM belonged. They refer to the clampdown as the Isaaq Genocide or "Hargeisa Holocaust". A United Nations investigation concluded that the crime of genocide was "conceived, planned and perpetrated by the Somali Government against the Isaaq people". The number of civilian casualties is estimated to be between 50,000 and 100,000 according to various sources, while some reports estimate the total civilian deaths to be upwards of 200,000 Isaaq civilians. Along with the deaths, Barre regime bombarded and razed the second and third largest cities in Somalia, Hargeisa and Burao, respectively. This displaced an estimated 400,000 local residents to Hart Sheik in Ethiopia; another 400,000 individuals were also internally displaced.

The counterinsurgency by the Barre regime against the SNM targeted the rebel group's civilian base of support, escalating into a genocidal onslaught against the Isaaq clan. This led to anarchy and violent campaigns by fragmented militias, which then wrested power at a local level. The Barre regime's persecution was not limited to the Isaaq, as it targeted other clans such as the Hawiye. The Barre regime collapsed in January 1991. Thereafter, as the political situation in Somaliland stabilised, the displaced people returned to their homes, the militias were demobilised or incorporated into the army, and tens of thousands of houses and businesses were reconstructed from rubble.