It took me seven trips, one to each country, but with my visit last weekend to El Salvador, I have now been to all seven Central American countries.
I visited El Salvador over a long weekend, and with limited time, I decided to base myself in Suchitoto, a colonial city about 30 minutes north of the capital, San Salvador. Suchitoto is a charming, safe, colonial city, with several good hotels and restauarants. I stayed at Los Almendros De San Lorenzo, a restored colonial structure, with a great pool and restaurant. The very friendly hotel staff arranged private cars to take me to three archaeological sites, Cihuatan, which is nearby Suchitoto, and Joya de Ceren and San Andres, around an hour from Suchitoto. Joya de Ceren, the country's only UNESCO World Heritage Site, contains the intact remains of pre-Colombian farming village that was overrun by a volcanic eruption, and for this reason, it is often referred to as the "Pompeii of the Americas." I have been to Pompeii, and there's a reason that Pompeii is not referred to as the "Joya de Ceren of Europe."
Now that I have been to all seven Central American countries, I would rank them, based on my very limited visits, as follows (I also indicate where I visited):
1. Guatemala -- Antigua and Tikal (I would enthusiastically revisit either of these places, both of which are UNESCO World Heritage Sites). I also visited Quirigua, the country's third UNESCO site, but its not as interesting as the other two.
2. Costa Rica -- San Jose (better than I had anticipated) and Monteverde (great birding, even for a non-birder like me).
3. Panama -- Smithsonian Tropical Research Institute, on an island created when the canal was formed, with lots of wildlife; great partial crossing of the Panama Canal; and wonderful old town (a UNESCO World Heritage Site.
4. Honduras -- Copan and its ruins (a UNESCO World Heritage Site).
5. Nicaragua -- Granada, a colonial city around an hour from Managua
6. El Salvador -- see above.
7. Belize -- while I liked the cave tubing in Caves Branch, I found the Cayes (Amergris and Caulker, both of which I visited) unappealing (next time I may make it further out on to the reef, where the diving is better).
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El Salvador -- Photos and Trip Report, and thoughts on Central America