Best ID references for single-celled organisms?

Hi all,
I’m lucky enough to have a compound microscope at home and I am dabbling with the idea of taking photos of single-celled organisms I might find in a drop of local pondwater, for example, and trying to ID them and post them to iNat as well. I have no real experience in this area and I’m expecting to encounter a cool but confusing array of interesting creatures! :) In preparation, I decided to purchase the surprisingly inexpensive two-volume “Illustrated Guide to the Protozoa, Second Edition”, but I have nothing at all that covers autotrophs and I’m not convinced the guide above is going to be easy to use.

Can folks please recommend their favorite and most useful web or book references for identifying single-celled organisms in freshwater or elsewhere? Ideally something with keys and that is copiously illustrated? I am in western North America.



You might consider seeing if you can get hold of the folks who run the Journey to the Microcosmos channel on Youtube and see what they recommend.


Thanks! What a cool series of videos! Those will help give me an overview of what I might see, I think, but I’m not sure how to ask a question of those folks on Youtube - seems like it’s a hugely popular channel and I doubt any comment I make will be replied to personally?

There are quite a few people on inat interested in single celled organisms. To get started, you can just upload your observations and leave at State of matter: Life and then add it to the Microscopy project and one of them might find it and give you an ID. The computer vision model can even occasionally identify things now. The microscopy project page also lists a bunch of references. I would add Freshwater Algae of North America, Ecology and Classification to the list as one of my favorites.


I love that channel too! The dramas, discoveries and surprises are incredible.

I’m also thinking of adding microscope observations to my iNat routine. Of course, seeing how since joining iNat my daily step count has dropped from 10,000 to 2,000, I’m a little bit frightened of what going micro would do to that.

“Woohoo! Six steps today! Doubled yesterday’s total!”


The videographer for the series is James Weiss, and he has a Instagram account called Jam’s Germs. He’s probably the better person to get hold of than the narrator.

The channel published the Microcosmos Field Guide which is, unfortunately, sold out at the moment.

James also published the The Hidden Beauty of the Microscopic World which is not sold out. It’s sort of a beginner’s introduction and isn’t really a field guide specifically.

Betsey Dexter Dyer’s A Field Guide to Bacteria has a good reputation, but it doesn’t cover all branches of microbial life. Interestingly, her approach includes non-microscope identification too.

There is the old Rainis and Russell Guide to Microlife, which you can find used for not too much money. It’s from 1996, so there may have been a number of taxonomic changes since then as there have been a lot of advances in the last nearly 30 years.

David Seamer’s books look like they may be useful, but it also looks like some of them may have an Australia focus.


In my experience, focusing just on microscopy has no impact on my step count. It takes only a couple seconds to collect a sample. Of course, then it takes at least several hours later on at home to go through them, which means I accumulate an ever increasing collection of samples that I have no time to look at. But on my hikes themselves, I’m the one getting annoyed when my companions stop to look at birds all the time.

Thanks so much for these references, much appreciated! I also just found this one, which looks quite useful - not sure if anyone else has experience with it - it’s UK-based, but seems likely to be applicable everywhere…

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