There are cities that developed historically as separate cities but in time they became one city. Here you can see such examples regarding capital cities of some countries.
Probably the best known examples of current capital cities that are actually two cities are the following, given in alphabetical order:
In some of them two cities are merged into one city, but some of them also split into two parts.
Why do cities merge or split?
In most cases this is simply because neighboring cities grow and eventually become one large city. But there are also historical reasons like in the case of Rome and Vatican.
In some cases this is due to political reasons, you will see some example below. All the cities listed above are given in the interactive map below. So zoom in to see the details of the cities:
This is currently the capital of Serbia. It used to be the capital of Republic of Yugoslavia as well, and before that the capital of Kingdom of Yugoslavia and also of the Kingdom of Serbia.
When it was in the Kingdom of Serbia, Belgrade was a border-city. Only rivers Sava and Danube were separating it from the Austrian-Hungarian empire. The nearest Austro-Hungarian city across the river Sava was Zemun city. Both Belgrade and Zemun are cities with a very long history that is measured in thousands of years.
During the Kingdom of Yugoslavia, Zemun was absorbed into Belgrade. This was in 1934.
Later, during Republic of Yugoslavia, Belgrade expanded across Sava river and a new city was built between Belgrade and Zemun, it was called New Belgrade. Nowadays, this is all one continuous big city with the name Belgrade.
Bogotá is the the capital city of Colombia, and one of the largest cities in the world. It is composed of Bogotá and Soacha. There are no barriers between the cities and you have a feeling this is all one single metropolis.
So here you have two cities that were historically Buda and Pest on the two sides of the Danube river, see the top picture above. If you check the page of this city on Wikipedia you will realize that it was Buda that was far more important in the past.
After 1849 when the Chain Bridge linking Buda with Pest was constructed across the Danube, these two cities were officially merged into Budapest in 1873.
In fact, there is also a third part known as Óbuda (Old Buda) that is in the present capital. Yet another peculiar detail about Budapest is that it was the twin capital (together with Vienna) of a dual Austro-Hungarian monarchy.
In this case, you have a brand new capital (Islamabad) built by a decision of the government in 1960s when they moved the capital from Karachi. If you follow the link you will see its picture which I took during one of several visits to the city.
The new capital was built next to its much bigger and old city of Rawalpindi. So you have a very modern capital, and its old large and crowded neighbor both growing in size and they are effectively one city but with a very different structure.
Here you have the capital London that includes the financial center the City of London, and the City of Westminster which includes the UK Parliament and Buckingham Palace.
This is one example where the original single city became two cities because of political reasons. In fact, the city split into two parts that are now in two separated countries.
The northern part of Cyprus is only recognized by Turkey. The city Nicosia/Lefkosia is divided in two parts and administered by two separate authorities. Note that Nicosia is also one of the oldest capital cities in Europe and this is the southernmost capital city in Europe.
The capital city of Canada, Ottawa, is at the confluence of the Ottawa River and the Rideau River, and it borders Gatineau, Quebec. The two cities form the core of the Ottawa–Gatineau census metropolitan area (CMA), and this is also the National Capital Region (NCR).
In this case you have Rome as the capital of Italy, and Vatican city as the capital of Vatican state. So this is the most peculiar situation, and reasons for this are both historical and political.
Perhaps you did not know, but Vatican became independent from Italy in 1929 with the Lateran Treaty. This is how it appeared as a city within a much larger city.
But when you see the map of Rome, you might think that this is one large metropolis. In fact, Vatican is the heart of Rome.
So these are capital cities that are actually two cities. But there are more examples where the capital is in fact a city that incudes several cities. One example is Indonesia’s capital city Jakarta. It is combined of 5 administrative cities.
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