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The 1769 transit of Venus was observed and coordinated by over one hundred astronomers around the world. How did they measure time so accurately, key to the observations having any scientific value? I find little information online regarding 18th century timekeeping devices. I assume that they were mostly using clocks intended for nautical navigation, as I think those were the most accurate of the era.

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The marine chronometer did not become widely available until the very end of the eighteenth century. They may play a part here, but they would have been rare and expensive. – dmckee♦ Jul 22 '12 at 18:37
@dmckee: Thank you for that excellent link! That does suggest that perhaps the lunar distance method was used. – dotancohen Jul 22 '12 at 18:41
Couldn't they use the precise time of high noon and longitude measurement? They know their longitude from maps, and high-noon from sundials. – Ron Maimon Jul 23 '12 at 5:43
Actually, longitude was not well-known in the 18th century. I understand that specifically Tahiti's longitude was known, that is why Cook went there. But even measuring high-noon would not be very precise. – dotancohen Jul 23 '12 at 5:57
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Land-based longitude had its own set of problems, mainly how to transport the clocks (not a problem for Cook). Land navigation was done using Lunar methods even after the seafarers switched to clocks. – dotancohen Jul 24 '12 at 5:46
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Since pre-historic times, it is the motion of stars which were used to measure time. Astronomers were well-aware of their motions and their relation to time. And as far as my knowledge goes, they had angle measuring instruments similar to modern day sextants by 18th century.

If you refer to any textbook in astronomy, one of the most important things they teach is how to keep time using motion of stars. This used to be every day(or night) practice in observatories.

There were assistants in observatories to calibrate time. It was a very important job in those times. This calculation had to be accurate. You can get the importance of this practice by your question.

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