Siem Reap and Phnom Penh cover Cambodia's two essential experiences — the ancient temple complex of Angkor and the modern capital confronting the country's more recent, harrowing 20th-century history.
This is Siem Reap's entire draw and one of the great sights on earth — Angkor Wat, Bayon Temple, and Ta Prohm Temple (with its tree roots overtaking the ruins) make up the Angkor Thom complex, best experienced at Sunrise at Angkor Wat. Phnom Penh has no equivalent ancient site of its own.
Phnom Penh's Tuol Sleng Genocide Museum and Choeung Ek Genocidal Center confront the Khmer Rouge era directly and are essential, if difficult, visits for understanding modern Cambodia. Siem Reap's history is almost entirely ancient rather than modern, with far fewer sites addressing the 20th century.
Phnom Penh's Royal Palace and Wat Phnom reflect its role as Cambodia's functioning modern capital, with the Independence Monument marking its 1953 independence from France. Siem Reap is a much smaller town whose infrastructure exists almost entirely to serve temple tourism.
Siem Reap sits beside Tonlé Sap Lake, Southeast Asia's largest freshwater lake, adding floating-village boat trips to the temple sightseeing. Both cities have their own airports; most visitors fly into one and out of the other, or connect by a scenic but longer bus ride along the lake.
Choose Siem Reap for Angkor Wat and the surrounding temple complex — reason enough on its own to visit Cambodia. Choose Phnom Penh for the capital's royal palace and its essential, sobering Khmer Rouge history. Most trips include both: temples in Siem Reap, then the capital's history and royal sites in Phnom Penh.