For example, how would you say "I thought you were in Japan"?

How about any other samples on how to use _omou_ in past tense?
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grammar usage verbs
How do you use "omou" in the past tense?
Nihon ni iru to omotteta noni.
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Well, I guess the past tense of 思｛おも｝う is 思った, thus "I thought" can be
directly translated to "思った".

According to
[tatoeba](http://tatoeba.org/eng/sentences/search?query=%E6%80%9D%E3%81%A3%E3%81%9F&from=und&to=und)
(Not the best example around, but still) :

`初{はじ}めは病気{びょうき}だと思った。 それは本当{ほんとう}だと思った。`

Are valid sentences and mean:

  * At first, I thought he was sick.
  * I thought it was true.

So 思った covers your use case :

` 日本にいると思った。`

To expand on the other answer : 思ってた would be akin to a progressive form, it
is a Verb-て+いる、but contracted. However, in this case the meaning is rather one
of "state-of-being", i.e. "思ってた" is closer in meaning to "I was in the state
of thinking" that "I thought". It is best to use it in your case, because (I
think) it puts more emphasis on the fact that you have changed your mind since
then. Depending on your intention, you can then add endings to your verb,
a.k.a のに. However, I am unsure to its sense.

By looking at [this link](http://maggiesensei.com/2012/06/20/how-and-when-to-
use-%E3%81%AE%E3%81%ABnoni-request-lesson/) and [this
question](https://japanese.stackexchange.com/questions/18063/the-%E3%81%AE-
in-%E3%81%AE%E3%81%AB-and-%E3%81%AA%E3%81%AE%E3%81%AB) it appears that のに is
similar to "although" or "even though" and the main sentence is often dropped.
In our case I guess のに would be expanded and translated to :

`Even though I thought you were in japan, (you are here)`
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Past tense of omou is omoimashita (formal ) or omotta (non formal).
**あなたは日本にいると思いました。** I thought you were in Japan.

there are a lot of verb conjugation websites out there I think it would be
easier if you know the the basic of Japanese verb conjugation. Try learning
the Te- form it would make you understand how easy it is to conjugate verbs.
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2015-02-10T05:16:31.093
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I'll assume that you aren't literally asking how to conjugate 「思う」 to past
tense (which simply put, is just 「思った」), but instead that you are actually
asking "how to use it in past tense".

* * *

What makes this complicated is that 「〜と思う」 doesn't mean "to think ~" (as in,
the state of holding some belief). Instead, it means something more like "to
have the thought ~" (as in, the instantaneous occurrence).

The state of "to think ~" then becomes 「〜と思っている」.

* * *

Using your example sentence "I thought you were in Japan", there are a lot of
translations. Let us consider these two:

> 日本にいると思った。
>
> 日本にいると思っていた。

Trying to explain the difference using English glosses probably will be a
futile exercise, but with the prior explanation in mind, this difference might
make sense:

  * The first (using 「思った」), expresses a degree of surprise or disbelief (because 「思った」 by itself means that you "just had the thought", and that notion of immediacy/recency indicates your surprise/disbelief).

  * The second (using 「思っていた」) is neutral.

So, depending on the context, you may choose the first or the second.

For example, if you live in America and someone you thought was in Japan walks
in the door, you could say something like

> え！？今日本にいると思った！  
>  "Huh?! I thought you were in Japan!".

On the other hand, if you're talking about what you thought in the far past,
where the surprise is no longer relevant, you would say something like

> 昨日電話した時、日本にいると思っていた。  
>  "When I called you yesterday, I thought you were in Japan."

* * *

Of course, "I thought you were in Japan." can be used in yet even more ways in
English, for example, "Man, I thought you were in Japan.", in which case you'd
say something like 「日本にいると思っていたのにな…」. I guess I would classify this usage
nuance as "expressing inconvenience".

Anyways, to save you from an even longer answer, let me conclude that if you
are trying to pay attention to nuance, then English and Japanese tend to be
pretty drastically different and translating between them can be pretty hard
for that reason. Hopefully this answer let's you know about the things you
might need to worry about with regards to 「思う」 in particular, at least.
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