The port's public reopening on Wednesday is the latest sign that the city's new Islamist rulers are trying to demonstrate their ability to rule a country just emerging from more than a decade of anarchy.
"From today on, the port is open and the world can send its goods here," Sheikh Abdulkadir Ali Omar, a deputy leader of the Islamic Courts Union, said.
Mogadishu International Seaport has been badly damaged by years of fighting and neglect but it is now ready to receive commercial traffic, Omar said.
The seaport has not been operational since 1995, when United Nations peacekeeping forces left Somalia amid rising political and clan-based violence.
The country's last effective central government was toppled in 1991 by rival commanders who then fought each other for control of the country.
Port opened for business
The port's reopening came 10 days after the Islamists captured the port town of Haaradere, about 300km (185 miles) of Mogadishu, which had been home to pirates who hijacked vessels in the Indian Ocean.
The government hopes that reopening the port will help improve Somalia's economy.
Somalia is poverty stricken after years of war
Omar Wehliye, the newly named manager of the port, said: "We are notifying the Somali people, especially businessmen, to use the seaport to ship their goods around the world."
Until last month, the port was controlled by rival commanders whose feuding militias prevented its use.
Businessmen and aid agencies have since then used a smaller, but poorly regulated, port outside the capital.
Mogadishu's international airport, closed more than 10 years, reopened a month ago.
Flights have been coming in and out of the airport daily, but it is unclear how much traffic the seaport would get. Somalia still has no coast guard or navy, and pirate attacks are frequent of the country's lawless coast.
Militia training camps set up
The Islamic Courts Union has also begun setting up a network of training camps that aim to create a force of well-trained soldiers to defend the government and enforce Sharia (Islamic law).
Sheikh Hassan Dahir Aweys, leader of the militia's Islamic courts, told 600 soldiers in Hilweyne military camp, about 20km north of the capital, Mogadishu, before they started training: "You are going to be trained to defend Somalia from internal and foreign aggressors.
"You are not going to kill people like the former warlords' gunmen killed indiscriminately."
Sheikh Hassan Dahir Aweys watches militiamen training
Aweys, 61, is designated a terrorist by the United States for suspected links to Osama bin Laden's al-Qaeda network and other related groups.
"This is the beginning, but thousands of other gunmen will be trained. You are the ones who will disarm civilians, restore law and order and help enforce Sharia law," he said.
In the space of a few months, Aweys' fighters have taken control of hundreds of miles of Somalia after defeating a US-backed militia in Mogadishu.
His forces are now pushing further east towards the Ethiopian border and northwards towards Somaliland and Puntland, two independent but internationally unrecognised mini-states, which have a degree of stability.