It is generally best to already be in Sihanoukville on the morning of your ferry to the islands (leaving yourself more time and avoiding any stress, problems, etc.). If you have a long journey to Sihanoukville, it is sometimes better to break the trip up.
For example, a private taxi from Phnom Penh to Sihanoukville takes 4 hours, so if you have a long flight to Phnom Penh, you should consider spending one night there.
Similarly, if you have a short flight to Phnom Penh and get a taxi to Sihanoukville immediately after, you should consider spending one night in Sihanoukville.
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