I’ve been doing a bit of research around the 1651 Czech Census that was taken immediately following the end of the Thirty Year’s War. Bohemia and Moravia had been predominantly Protestant prior to 1624 and the Census was ordered by the Austrian Catholic Habsburg rulers to determine the likelihood of converting the population back to Catholicism.
The Census documents are a valuable source of information for genealogical research, and are divided according to feudal province. They are available electronically for free from the Czech National Archives:
The formal Czech name for the Census is Soupis Poddaných Podle Víry z Roku 1651 (“List of Subjects According to Faith from the Year 1651”). A Full Index for the documents is also available.
The modern Czech provinces are slightly different, so it’s useful to reference this list against a map like the following, which illustrates how Bohemia looked at the time of the 1654 Tax Rolls (e.g., Berní rula):
The numbered regions on this map do not correlate perfectly with the eleven provincial census registers from 1651 listed above, but they should give a general sense of the local geography.
The numbered regions listed on the map are as follows: 1. Boleslavsko, 2. Hradecko, 3. Chrudimsko, 4. Čáslavsko, 5. Kouřimsko, 6. Bechyňsko, 7. Prácheňsko, 8. Plzeňsko, 9. Žatecko, 10. Litoměřicko, 11. Slánsko, 12. Rakovnicko, 13. Podbrsko, 14. Vltavsko, 15. Loketsko, 16. Pražská města, 17. Kladsko, 18. Chebsko, 19. Ašsko.
Additional detailed maps of some of the provinces are also available:
Most of these maps are color-coded according to a scheme similar to:
- Stav duchovní — Monastic or clerical estate
- Stav panský — Noble or aristocratic estate
- Stav rytířský — Knightly or military estate
- Stav městský — City or town municipal jurisdiction
Most, if not all, of the regional census documents listed above includes a table translating German-to-Czech place names, so you have a bilingual reference to city and village names — e.g., you can deduce that Liberec is also Reichenberg, or that Okna is also Wocke, which might not be so obvious just by looking at the respective names.
The following German-Czech Ortsnamenverzeichnis can also be helpful — it appears to be as complete as the larger Czech Census PDF documents, and it can be searched electronically much more easily:
The Czech Republic is a country where every province, with the exception of the central Prague district, touches a foreign border — moreover, four of those five borders have historically been German (Silesia, Saxony, Bavaria and Austria). This has changed since the end of WWII with the transfer of Silesia back to Poland, but a knowledge of German Ortsnamen in Bohemia can still prove very useful in doing historical research.
The following map is immensely helpful for doing actual genealogical research:
Birth and death records will generally be kept in the regional archive (indicated above) where the individual was born or died, so you may have to jump around between different regional archives to track down all your relatives.
Finally, even though you manage to track down the correct archive, the battle has only just begun — even if you’re fluent in both Czech and German!
Reproduced above is the frontispiece to a matricula from 1723 kept at the parish church in Červený Kostelec in northeastern Bohemia near Náchod. Even if you think you know Latin, good luck deciphering that script! 
The actual genealogical records themselves can be an even bigger challenge.
From the 19th-century onwards the records are generally kept in a more standardized format, and recorded in more legible German or Czech, but if you’re looking for earlier records it may be worthwhile to hire a local, professional genealogist who’s trained in reading these older, hand-written Latin scripts. 
Update — October 11, 2020
Many matrices and archives have been digitized, the following Web site is an excellent resource for locating the various regional archives:
However, the link to the Zámrsk archives in northeastern Bohemia is outdated, to reach those archives use the following links:
Update — October 20, 2020
The Litoměřice Archives are available online here:
- Reproduced here under Fair Use.
- As far as I know, all of the documents and images cited here are in the public domain. Nevertheless, I found many of these documents on the following Web site: https://www.ahnenheidrich.eu/