Black egg yolks...

It possibly could be from a fungus or bacteria in the egg such as staphylococcus, E.coli, or pseudomonas, especially if there is a rotten odor. Eating certain weeds can cause a blue green color. Here is some reading:
https://www.backyardchickens.com/articles/common-egg-quality-problems.65923/
http://www.thepoultrysite.com/publications/1/egg-quality-handbook/34/rotten-eggs/
http://www.hobbyfarms.com/the-freshly-laid-rotten-egg/
https://www.backyardchickens.com/th...s-laying-smelly-eggs-with-black-yokes.369427/
 
Here is my thought how to find the culprit, given if its an internal issue and not an external. Of course first you need to crack all the freshest eggs to determine if its external or internal. But week pretend it's internal for a minute.

I'll use my own flock as the example

Btw how many chickens do you have? And do you have a second coop or pen you can use for separating?

I have 18 chickens but only 10 are laying. So we will focus on 10 and pretend that all lay roughly the same color shell since you indicate you can't tell who laid it.

Of the 10 you could seperate 5 and 5 and check each group of eggs seperatly. Possibly for 2-3 days if you can confirm you have gotten at least 1 egg from each. Pretend group A had all good eggs but group B had a bad age. You would need a third pen to seperate group B into 2 smaller groups. B1 (2 hens) B2 3 hens. From here well say the culprit is in B1 all eggs from B2 are normal they can be released back to the main flock. You only need to seperate the 2 from B1 to find which one is having an issue.

Now if you can't seperate them into groups but can do 1 or 2 singles at a time. That would work also but may take longer. Just place each one in the pen untill she lays and you can check it. You might need to find a way to mark your hens during this to make sure you get each one. I would do every hen regardless of finding the culprit just to insure that there is infact only 1 offender. The good thing about doing singles though is you might beable to seperate them within the normal flock (like a broody or chick pen) so no one needs to be reintegrate later on, just released and replaced with the next hen... as for marking i have blue kote on hand something like that could be used to spray thier back or tail so they are easily identified as cleared, though it stains and they might be purple untill next molt...
 
Thank you for all of the feedback and the links! (I will be reading the links later.)

1. There were no apparent cracks in the bad eggs.
2. There was no bad odor at the time the eggs were collected and stored.
3. They were stored together, in reused egg CLEAN cartons.
4. There are 29 hens (& 3 roo's) in this flock. Separating them out now would be a bit challenging. I would have to put some major projects on the back burner to do so. (I still have two animal houses to finish winterizing. I have a turkey house that needs to retrofit to move a new flock into. Etc.) And some of the training (like for the dogs) in progress would have to be stopped until the egg thing is figured out. AND I would need to create a separate pasture for them, as well as set up new housing/nests. All doable but it would take time and resources from the current projects.
5. I had planned to do my wonderful zip tie sit out starting next week or two. I sit in the coop/animal house during egg laying time and put a zip tie on the legs of girls laying eggs. One per day. At the end of the week, I can see who has laid and how many eggs were laid. I usually do two weeks of this - some girls take a bit longer to lay after a molt. The girls not laying at all are culled or moved to a new flock to help train newbies. I can modify how I do this and put a number on the zip tie (like #1 for one girl, #5 for another girl) and put the same number on the egg. That would allow me to associate bad eggs with a chick
6. Ugh. More work! :tongue And a great learning experience. :bun
7. I may need more coffee and/or sleep.
8. I am not renumbering my post, so this goes at the end. None of the eggs had poop on them. I collect the eggs and they immediately go into an egg carton for the day. I will start adding a date collected piece of paper to each carton. When I sell/give eggs, I always give the freshest eggs. No complaints.
9. I go through eggs pretty quickly. I had the extra eggs because someone had asked for a bunch of eggs, so I had reduced my daily usage to make sure there would be enough eggs. Always gave the freshest eggs and kept the oldest for me.
10. I noticed that the eggs had spots on them -- that appeared AFTER they sat in the egg carton. Very faint, faint circles.
11. I noticed that a few of the eggs (but not all of them) actually seeped gunk from inside to the outside. They had kinda gunk on the shell that wasn't there when I put them in the egg carton. The egg cartons sit on my kitchen counter and don't get moved or bumped into. They are not in direct sunlight. Temp is pretty constant.
 
I would say just go through your eggs for a few days as normal and see if funky eggs continue to show up first. Maybe it was just an out side contaminate...
 
Some eggs could have some microscopic cracks that allows entering of microbes into the eggs. In this situation the egg will rot very quickly and the smell will be awful! (It is the Hydrogen sulfide caused by the microbial activities on the yolk)

I think Benny hit the nail on the head... at first read. I was of the understanding that it was a single egg. But, Sara, your last post made me think it was an issue with more than one egg. So, bacterial contamination, either from inside or outside the egg seems to be the issue. I had an egg in the bator that went bad once. It also started developing dark spots on the shell, and IIRC, it was oozing through the pores. I actually found it by holding each egg up to my nose and sniffing it!

If a chicken has a diet high in acorns, it can turn the yolk black. But your egg was definitely rotten. So, this is most likely not the issue. I'm sure other plants, if a lot are ingested can do funky things to the egg as well.

Will be watching to see if you have anything further to report.
 
I am curious if you ever figured out the black yolk thing. I got one yesterday while all the rest were fine. No smell - I don't think. I unfortunately cracked it in with about a dozen others (my bad) and quickly through the whole pan out. So gross! Now I'm worried about eggs I've given to others. Course I haven't had any other issues. ?
 

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