As delighted southern Sudanese voted in a long-awaited referendum on independence, visitors to the north and south could be forgiven for thinking they were already two separate countries.

Far from the orange dusty landscape of Khartoum, newcomers landing at the airport in south Sudan’s capital Juba wander off the runway to be greeted by a smack of wet, humid heat driven by the surrounding lush tropical forests.

Beer adverts and often drunk soldiers adorn the few Tarmac roads in the would-be capital of what is likely to be the world’s newest nation state, a culture shock to anyone coming from the Islamic north where alcohol is banned.

Visitors enjoy Nile-side restaurants where they can sip a glass of wine and eat pork unavailable up north. The south’s population is mostly Christian or follows traditional religions.

African music blares throughout the town’s markets, run by Ugandan and Kenyan traders. Residents shout at each other in an Arabic dialect almost incomprehensible to northerners.

In the north, Arab music or Islamic verses are heard in the minibuses which hurtle around the capital.

But window dressing aside, south Sudan has effectively been operating as a separate nation since it was given a semi-autonomous government under a 2005 peace deal which ended the bitter north-south civil war — Africa’s longest.

Juba then set about creating what has become a state within a state.

“Is (the south) ready to govern itself? That’s what they’ve been doing for the last six years, doing just that,” David Gressly, the top U.N. official in the south, said.

It has its own constitution, a separate central government,  10 state governments all answering to Juba, its own parliament and even its own laws.

The two regions even have different banking systems – the north operates under Islamic sharia law while the south uses a conventional banking system. Few northern banks operate in the south, dominated by new southern Sudanese or East African banks.

Ministries which began in pre-fabricated buildings often with just a minister in a lonely office with a few tea ladies and cleaners for company have become fully functioning institutions, complete with staff.

“Frankly, the started with a president and a vice president and built everything from there,” Gressly said.

Khartoum’s foreign ministry was enraged when the south began opening “liaison offices” around the world which effectively functioned as embassies for the southern government.

And Khartoum complained that Juba was not transferring any of the money it was collecting from customs or immigration.

Juba in fact kept an entirely separate immigration system. Sudan visas, notoriously difficult to get, were bypassed by visitors who would get “Government of Southern Sudan” permits in Nairobi, travel to Juba and then get on a domestic flight to Khartoum.

One friend who entered the south overland across the Ugandan border got a “New Sudan” stamp on his passport from immigration. When Khartoum’s interior ministry saw the stamp, they panicked, fined him and stamped his passport with “British infiltrator”.

“This is crazy – we are supposed to be one country but we can’t coordinate our immigration!” One Khartoum official grumbled to me as yet another journalist arrived with papers issued in the south, but not recognised in the north.

One wonders what, other than perceptions, will actually change once the south becomes independent on July 9.