Obsidian and Markpad start from the same idea: notes get more useful when they're linked, not filed. Past that, they're built on opposite bets. Obsidian bets that you'll want to shape the tool yourself. Markpad bets that you'd rather not have to.
Local files vs. local-first encryption
Obsidian stores your notes as plain Markdown files on your own disk. That's a real strength — the files are yours, readable by any editor, and outlive the app if you ever stop using it. But "on your disk" isn't the same as private. A note in Obsidian sits on disk unencrypted unless you add a plugin and manage that yourself; anyone with access to the machine, the file system, or an unlocked backup can open it.
Markpad works the other way. It's a browser-based vault, and every note is encrypted with AES‑GCM on your device before it's ever saved, using a key derived from your passphrase. There's no plugin to install for that and no setting to remember to turn on — it's just how notes are stored, from the first one you write.
Plugins vs. defaults
Obsidian's real power is its plugin ecosystem — thousands of community plugins that can turn it into a task manager, a spaced-repetition system, a citation tool, nearly anything. That flexibility comes with setup: choosing plugins, configuring them, keeping them updated, and occasionally troubleshooting when two of them disagree.
Markpad doesn't have a plugin store, because it isn't trying to be a platform. Backlinks, tags, folders, and daily notes work the same way for everyone, out of the box, with nothing to configure before you can start writing.
Obsidian gives you a workshop. Markpad gives you a finished room.
Cost and where you write
Obsidian is free for personal use, with sync and publishing sold as separate paid add-ons if you want your notes across devices or on the web. Markpad is a single $5 USD/month plan, browser-based by design, so there's one price and nothing extra to add later — no local install, no separate sync tier.
Neither approach is wrong. If you want to shape your note-taking system plugin by plugin and keep files on disk under your own management, Obsidian rewards that. If you'd rather have backlinks, daily notes, and encryption working the moment you open a tab — with nothing to configure — that's the gap Markpad is built to fill.