Obsidian holds a narrow lead over Logseq for Markdown notes with bi-directional linking. Logseq closely follows as an open-source, privacy-focused outliner for connected notes.
If you want a note-taking app with bi-directional linking and Markdown, I'd start with Obsidian. It's particularly good if you want to build a personal knowledge base where notes link to one another and you can see which other notes reference each idea.
Here are the best options, depending on how you like to take notes.
Top note-taking apps to consider
1. Obsidian
(Best overall)
Stores notes as local Markdown files, supports backlinks and internal links, and offers a graph view of your connected notes. You can keep your files and choose how to sync them.
Best for: Long-term knowledge management, research, journaling, and personal wikis.
Designed around linked notes and an outline-style workflow. It supports backlinks, page links, block references, and Markdown.
Best for: Daily notes, meeting notes, research, and connecting individual bullet points across documents.
Website:
3. Joplin
A strong option if you prefer a traditional notebook-and-folders structure with Markdown editing and open-source software. Its linking workflow is less centered on a connected knowledge graph than Obsidian's.
Best for: Organized notes, clipping web pages, and a more conventional notebook experience.
Website:
4. Anytype
A more visual, object-based approach to organizing and connecting information. Worth considering if you like structured pages and relationships, though it is not as straightforward a plain-Markdown file workflow as Obsidian.
Best for: Visual organization, connected information, and customizable personal workspaces.
Website:
Quick comparison
App
Bi-directional links
Markdown
Main advantage
Obsidian
Built in
Native files
Flexible, powerful knowledge base
Logseq
Built in
Supported
Excellent block-level linking
Joplin
Via plugins for richer backlinks
Native editor
Traditional notebooks
Anytype
Object relationships
Import/export
Visual, structured organization
Joplin's core Markdown workflow is documented officially, and its plugin directory includes tools for backlinks and bidirectional links.
My recommendation
Choose Obsidian if you want the simplest combination of Markdown files, backlinks, cross-linked notes, and long-term portability.
Choose Logseq if you think in outlines, daily journals, and individual blocks of information rather than longer documents.
One question that would help narrow it down: what devices will you use it on?
Joplin : Best open-source Evernote/Obsidian alternative if you want a more traditional hierarchical folder layout combined with Markdown and an optional web clipper. While its bi-directional linking isn't as heavily emphasized as Obsidian's or Logseq's, it supports internal note links cleanly.[](https://www.tinystartups.com/blog/best-markdown-note-taking-apps)
Yes. If Markdown files + bi-directional links/backlinks are the key requirements, I’d shortlist these:
App
Best for
Markdown files
Bi-directional links
Obsidian
Best overall
✅ Native .md files
✅ Excellent
Logseq
Outliners / daily journaling
✅ Markdown/Org
✅ Excellent, including blocks
SiYuan
Block-based knowledge management
⚠️ More database-oriented
✅ Excellent
Zettlr
Research / academic writing
✅ Native Markdown
✅ Good
Joplin
Open-source + syncing
✅ Markdown-based
⚠️ Less central to its design
🥇 My recommendation: Obsidian
Obsidian is probably the closest match to what you're describing. Your notes are ordinary Markdown files in a folder you control, while Obsidian adds wiki-style [[links]], backlinks, graph visualization, properties, search, and a huge plugin ecosystem.
One particularly nice feature is that backlinks aren't merely a graph visualization: Obsidian can show both linked references and unlinked mentions for the current note.
It also supports regular Markdown links if interoperability is more important to you than Obsidian's [[wikilink]] syntax.
🥈 Logseq if you think in outlines
Logseq is my pick if your notes naturally look like nested bullet points and daily journals. Its distinctive advantage is block-level linking and references, so you can connect individual thoughts rather than just entire documents.
What I'd choose
Want the safest, most flexible long-term choice → Obsidian
Want a more database/block-oriented system → SiYuan
Doing academic/research writing → Zettlr
Want open source with a more traditional notes workflow → Joplin
If your priority is specifically “I want a folder full of portable .md files that I can still use if I abandon the app”, I'd choose Obsidian. Current comparisons also consistently distinguish it from apps that merely edit like Markdown but store notes in a proprietary database.
If you tell me whether you're on Windows, Mac, Linux, iPhone, or Android, I can narrow this down to the 2–3 best choices for your setup, including sync options and pricing.
