The short answer. Zotero is the reference manager: collect sources, annotate, cite in a word processor and produce a bibliography in the right style. Highlights is the PDF reader built for research, with annotations that export. PDF Archiver is the tagging and archiving tool for a folder of papers. Tropy is for photographs of documents — archives, letters, manuscripts — where the metadata is provenance rather than publication. Klib manages highlights from Kindle and iBooks, which is a reading workflow rather than a citation one. Wokabulary is the vocabulary trainer, which is a different kind of collection entirely. The dividing question is whether you are producing citations or keeping notes, because a reference manager is a citation engine and everything else here is a reading tool.
This guide covers 6 reference managers for macOS. Every fact below is drawn from the same verified records that back each app’s own page. The recommendations are our editorial judgment, not payment.
Quick comparison
| App | What it is | Pricing | Licence | Version |
|---|---|---|---|---|
| Highlights | productivity app | Free | not published | — |
| Klib | productivity app | Free | not published | 2.0.9 |
| PDF Archiver | file management tool | Open source | not published | 4.6.0 |
| Tropy | design tool | Open source | not published | 1.17.3 |
| Wokabulary | productivity app | not published | not published | 8.1.3 |
| Zotero | productivity app | Free | not published | 10.0.5 |
What actually decides this
- Cite or read. A reference manager produces a bibliography that a word processor can consume. A reader produces annotations. The two are often confused because both store PDFs, and only one of them will save you from retyping a citation.
- Where the library lives. A local Zotero library with a sync option is portable. A cloud-only library is convenient and depends on a service. For a thesis measured in years, the local file is the safer base.
- What the annotation can do. Highlighting is a colour. An annotation with a comment and a page reference is a note you can use. An annotation that exports into a citation manager is a research workflow.
- Whether it handles non-text sources. A photograph of a letter, a manuscript page and a map are sources with provenance and no DOI. A tool built for journal articles has nothing to put in those fields.
- What the export formats are. BibTeX, RIS, CSL JSON and a formatted bibliography are four outputs. If the writing happens in LaTeX, Word or a Markdown editor, the export decides whether the tool fits at all.
Our picks
- Zotero — Its record describes collecting, organising, annotating, citing and sharing research, which is the citation case. Choose it when you need citations and a bibliography.
- Highlights — Its record describes a PDF reader for research across Mac, iPad and iPhone, which is the reading case. Choose it when the main activity is reading and annotating papers.
- PDF Archiver — Its record describes tagging and archiving, which is the archive case. Choose it when you want to tag and archive a folder of papers.
- Tropy — Its record describes research photo management, which is the provenance case. Choose it when the sources are photographs of documents.
- Klib — Its record describes managing highlights for Kindle and iBooks, which the reading-highlights case. Choose it when your highlights come from Kindle and iBooks.
The apps
Highlights
Highlights is a productivity app for macOS. The PDF Reader for Research on Mac, iPad & iPhone. It is free.
Full profile and verified facts for Highlights →
Klib
Klib is a productivity app for macOS. New way to manage highlights for Kindle and iBooks. It is free.
Klib is listed with current version 2.0.9.
Full profile and verified facts for Klib →
PDF Archiver
PDF Archiver is a file management tool for macOS. Nice tool for tagging and archiving tasks. It is open source.
What it does. Macobserver - How to Archive PDFs with PDF Archiver. iFun - Kostenloser iOS-Kompagnon ergänzt die Mac-App. Netzwelt - PDF-Dokumente einfach verwalten. Sir Apfelot - PDFs verschlagworten, ordnen und archivieren.
PDF Archiver is listed with current version 4.6.0.
Full profile and verified facts for PDF Archiver →
Tropy
Tropy is a design tool for macOS. Research Photo Management. It is open source.
What it does. Tropy is free open-source software that allows you to organize and describe photographs of research material.
Tropy is listed with current version 1.17.3.
Full profile and verified facts for Tropy →
Wokabulary
Wokabulary is a productivity app for macOS. Collect, practice, and organize your individual foreign language vocabulary. Its pricing is not published.
What it does. The best app to learn foreign language vocabulary on your Mac, iPhone and iPad. With spaced repetition learning, multiple quiz modes, and motivating statistics.
Wokabulary is listed with current version 8.1.3.
Full profile and verified facts for Wokabulary →
Zotero
Zotero is a productivity app for macOS. Free tool to collect, organize, annotate, cite, and share research. It is free.
What it does. Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
Zotero is listed with current version 10.0.5.
Full profile and verified facts for Zotero →
How to choose
- Free of charge. Highlights, Klib and Zotero — no payment is required.
- No licence fee, source available. PDF Archiver and Tropy — the source can be read and, under the terms of each licence, reused.
- Pricing not published in our data. Wokabulary — check the developer’s own site before assuming anything about cost.
Open source: PDF Archiver and Tropy (2 of 6).
Common mistakes
- Reading papers for years in a tool that cannot export a citation.
- Storing annotations in a PDF that a co-author will overwrite.
- Using a journal-article manager for archival photographs and leaving the provenance fields empty.
- Keeping the library in one app with no export and calling it a research archive.
How this guide was put together
Each app’s facts come from its own record: the developer’s own pages and repository, the App Store listing where one exists, and the documentation, each with a source grade and an access date. Where a fact rests on the developer’s own statement rather than on something we verified independently, the sentence says so. Where our data has no value for something, the guide says “not published” instead of guessing.
A price appears here only where the record carries one from a stated source; the guide never estimates one, and it records the pricing model alongside so the two can be read together. Prices change and vary by region, so each app links to its own page for the current detail.
The facts and the recommendations are kept apart on purpose. Everything in the app entries, the comparison table and the answers above is composed from the records. The short answer, the criteria and the picks are our editorial judgment: they reflect what we would choose and why, and they are not paid for. Where we make a recommendation we name the condition it applies under, because we do not call anything “the best” without explaining the criteria.
Frequently Asked Questions
How do I choose between these reference managers?
There is no single answer — it depends on what you need. This guide covers 6 reference managers: Highlights, Klib, PDF Archiver, Tropy, Wokabulary and Zotero. They differ mainly in pricing model, licence and the trade-offs each one carries. Pick by the trade-off you care about rather than by rank.
Are these reference managers free?
Pricing across this group: free (Highlights, Klib and Zotero), open source (PDF Archiver and Tropy) and not published (Wokabulary). Where we list pricing as not published, the developer does not state a model we could verify — check their own site before assuming anything about cost. We quote a price only where the record carries one from a stated source, and we never estimate one. Prices change and vary by region and by store, so always check the developer’s own page for the current figure.
Which of these reference managers are open source?
PDF Archiver (not published) and Tropy (not published) are open source.
Do these reference managers support Apple Silicon?
Our data does not carry an explicit Apple Silicon statement for any app in this group, so we do not claim one. The absence of a statement is not the same as the absence of support.
How do I choose between them?
Start with how you pay: the guide groups these apps by pricing model, because the budget is the constraint most people actually have. Then check the trade-offs listed for each app: the limitations are the part that decides most people’s choice, because they describe what the app will not do for you.
