tukue no ue ni boorupen ga nihon arimasu.

机 means desk, 上 means top / above / upper part, and の links the two nouns.

So 机の上 literally means the top of the desk, or more naturally, on the desk.

In this pattern, A の B often means:

• B of A
• B belonging to A
• B related to A

So here:

• 机の上 = the desk’s top = the top of the desk

に marks the location where something exists.

With あります and います, Japanese commonly uses:

• place + に + thing + が + あります / います

So:

• 机の上に = on the desk
• ボールペンが二本あります = there are two ballpoint pens

A common learner question is whether で could be used instead. Normally, no:

• に = where something exists
• で = where an action happens

Since this sentence is about the existence of pens, に is the correct particle.

が marks the thing that exists in an existence sentence.

In a sentence with あります or います, the basic pattern is often:

• place に thing が あります / います

So here:

• ボールペンが = as for the thing that exists, it is ballpoint pens

This does not mean が is always the only option in every situation, but in a neutral sentence introducing what is there, が is very natural.

Compare:

• 机の上にボールペンが二本あります。
  = There are two ballpoint pens on the desk.

If you used は instead, the nuance would change, often making ballpoint pens the topic rather than simply identifying what exists.

Japanese uses different existence verbs depending on whether something is animate or inanimate.

• います is used for people and animals
• あります is used for things and inanimate objects

Because a ボールペン is an object, the correct verb is あります.

Examples:

• 猫がいます。 = There is a cat.
• 本があります。 = There is a book.

二本 means two long cylindrical objects.

Japanese usually uses a counter when counting things. You normally do not just put a bare number before a noun the way English does.

Here:

• 二 = two
• 本 = counter for long, thin objects

So 二本 means two of a long, thin object.

Common things counted with 本:

• pens
• pencils
• bottles
• umbrellas
• trees

Since a ballpoint pen is long and thin, 本 is the correct counter.

Counters often change pronunciation depending on the number attached to them.

For 本, some common readings are:

• 一本 = いっぽん
• 二本 = にほん
• 三本 = さんぼん

So although the kanji is the same, the sound changes. This is very common with Japanese counters, and it is something learners usually need to memorize through practice.

In Japanese, a counted noun often appears in a structure like:

• noun + が + number-counter + verb

So:

• ボールペンが二本あります

This is very natural Japanese.

English says:

• There are two ballpoint pens

Japanese more literally works like:

• As for ballpoint pens, there exist two (of them)

You may also see numbers placed before nouns in other patterns, but with existence sentences like this, noun + が + counter is very common.

Yes, but the nuance changes.

Compare:

• 机の上にボールペンが二本あります。
  This neutrally states that there are two ballpoint pens on the desk.

• 机の上にはボールペンが二本あります。
  Adding は after the location gives contrast or emphasis, something like:
  On the desk, there are two ballpoint pens
  or
  At least on the desk, there are two ballpoint pens

• ボールペンは机の上に二本あります。
  This makes ballpoint pens the topic and sounds different in focus.

So が is the most straightforward choice in the original sentence.

This is because Japanese and English divide space differently.

上 literally refers to the upper area or top part of something. In a phrase like 机の上, it means the area on top of the desk.

In natural English, we usually say:

• on the desk

So the translation uses on, even though the Japanese expression is built from desk + top.

This is very common:

• テーブルの上 = on the table
• ベッドの上 = on the bed
• 棚の上 = on the shelf / on top of the shelf

No. Standard Japanese is normally written without spaces between words.

So the sentence would usually appear as:

机の上にボールペンが二本あります。

Spaces are often added in beginner materials to make the structure easier to read. They are a learning aid, not standard writing.

The pattern is:

• place + に + thing + が + number-counter + あります

Applied to this sentence:

• 机の上に = on the desk
• ボールペンが = ballpoint pens
• 二本 = two long thin objects
• あります = exist / there are

So this is a very useful model for making similar sentences, such as:

• 箱の中にりんごが三つあります。 = There are three apples in the box.
• 公園に犬が一匹います。 = There is one dog in the park.

It is a core beginner pattern for saying that something exists somewhere.