The short answer
If the file is one of your notes, read it in Obsidian. If it is a file from somewhere else, one you want to read as it is, where it is, without adding its folder to your vault, open it in MarkdownPaper.
Where Obsidian is the better choice
- A notes system. Links between notes, backlinks, a graph of how they connect, search across the whole vault. MarkdownPaper keeps a library of documents you have opened, and nothing links them.
- Writing. Live Preview hides Markdown's symbols as you type, and Source mode shows them all. MarkdownPaper's editor is for fixing a document, not for keeping notes in.
- Every device. Obsidian runs on Mac, Windows, Linux, iPhone and Android, with its own paid Sync between them. MarkdownPaper's desktop app is for Mac and Windows, and its web reader covers the rest.
- It follows the whole vault. Obsidian refreshes when any file in the vault changes on disk. The MarkdownPaper desktop app follows the one document you have open.
- It is yours to extend. A large library of community plugins and themes can change almost anything. MarkdownPaper has three paper stocks and no plugins, on purpose.
- It is free for personal and commercial use, with no account.
Where MarkdownPaper is the better choice
- One file, from anywhere, as it is. Obsidian works on vaults: its help
describes opening a folder as a vault, and opening a single file outside
one is a long standing
feature request
on its forum. The MarkdownPaper desktop app opens
any
.mdfile with a double click in Finder or File Explorer, and the web reader opens one you drop on it. - Nothing added to your folders. Obsidian keeps each vault's settings in
a
.obsidianfolder at the root of the vault, which in a code repository is one more thing to keep out of version control. MarkdownPaper keeps its records in its own data folder, and opening a file never changes it. - A page, not a workspace. Text is set to a measure counted in characters, 74 by default, in a serif made for reading, and you drag either edge of the page to change it. The contents sit in the page margin, and the few controls fade out while you read.
- Nothing to set up. No vault to choose, no plugins or theme to pick. Tables, highlighted code, footnotes, KaTeX math and Mermaid diagrams are typeset from the start.
- Handing it on. Print sets real page margins for a PDF, a saved HTML file carries its own fonts, and a rendered page copies into Google Docs with its tables intact. Someone without the app can read the same document in a browser.
Side by side
| Obsidian | MarkdownPaper | |
|---|---|---|
| Built for | Notes that link to each other | Reading a finished document |
| Opens | Folders, as vaults | Single files and pasted text; folders in the desktop app |
| Where it runs | Mac, Windows, Linux, iPhone and Android | Any browser, or a Mac and Windows app |
| Adds to your folder | A .obsidian settings folder | Nothing |
| Follows file changes | The whole vault | The open document, in the desktop app |
| Math and diagrams | MathJax and Mermaid | KaTeX and Mermaid |
| Extending it | Community plugins and themes | Not extensible, on purpose |
Price
Obsidian is free for personal and commercial use. Its optional Sync costs 5 month to month, Publish costs 10 month to month, and a commercial license, $50 per user a year, is a way to support it rather than a requirement. Those are the prices on Obsidian's pricing page on the date at the top of this page.
The MarkdownPaper desktop app: Coming soon to the Mac App Store and the Microsoft Store. $6.99 launch price, paid once, with no subscription. About the desktop app.
The MarkdownPaper web reader is free, with no account and no limits.
Using both
Keep your notes in Obsidian. Use MarkdownPaper for the files that are not
notes and should not become them: the PLAN.md an agent is rewriting in a
project, a README you are reviewing, a document you were sent. Keep the
desktop app open on a file while an agent works and the page follows it.
MarkdownPaper also reads a note straight out of your vault, since a vault is only a folder of Markdown files. Open one there when you want to read it as a page, or print it. It will not follow Obsidian's own links between notes.
If what you want is a Markdown editor rather than a notes system, the Typora comparison covers that.
Questions
Can Obsidian open a single Markdown file?
Obsidian is built around vaults, so to read a file you open its folder as a vault or move the file into one you have. Its help describes no way to open a single file on its own. MarkdownPaper opens any single file, from any folder, without asking where it belongs.
Why does Obsidian add a .obsidian folder?
It holds that vault's settings, such as its theme, plugins and layout.
It is hidden on most systems. If you open a code repository as a vault and do
not want the folder committed, add .obsidian to the repository's
.gitignore.
Is Obsidian free?
Yes, for personal and commercial use. Sync and Publish are paid services on top, and a commercial license is optional.
What should I use to read the files Claude Code or Codex writes?
Coding agents leave their plans and notes as Markdown files in the project folder, so a reader that opens files where they are fits them best. The MarkdownPaper desktop app opens them with a double click and follows the file as the agent rewrites it, and the AI Markdown reader page covers Markdown pasted from a chat instead.