I’ve executed over 17, 000 notarizations since I became a notary in 2012 and I established a policy from the beginning to obtain a thumbprint for every notarization, regardless the nature of the document.  It’s a great fraud deterrent and positively identifies the signer.  From my perspective, it provides protection for both the signer and the notary.
I have had only one individual refuse to submit a thumbprint.

In CA, if the document affects the transfer of real property or is a Power of Attorney document, the notary is required to obtain a thumbprint.
It isn’t required for other documents, but is recommended by the National Notary Association:

“It is a strong deterrent to forgery, as it represents absolute proof of the signer’s identity and proves the signer was present before the Notary.”

In 1996, CA passed the following law, California Government Code 8206 (a)(2)(G):
“If the document to be notarized is a deed, quitclaim deed, deed of trust, or other document affecting real property, or a power of attorney document, the notary public shall require the party signing the document to place his or her right thumbprint in the journal. If the right thumbprint is not available, then the notary shall have the party use his or her left thumb, or any available finger and shall so indicate in the journal. If the party signing the document is physically unable to provide a thumbprint or fingerprint, the notary shall so indicate in the journal and shall also provide an explanation of that physical condition. This paragraph shall not apply to a trustee’s deed resulting from a decree of foreclosure or a nonjudicial foreclosure pursuant to Section 2924 of the Civil Code, nor to a deed of reconveyance”

In the case of my reluctant thumbprint client, the document in question was not a deed or POA.  After I diligently recorded his full name, address, driver license number and date of birth in my journal, he expressed he was uncomfortable with giving his thumbprint, citing concerns of identity theft.

The client had complied with all the laws that govern notarization and his refusal to give a thumprint was not legal cause to refuse him service.  If his document had required it, however, I would have been unable to proceed.

Because I feel it demonstrates due diligence on my part and provides positive proof of the signer’s identity, which is a powerful fraud deterrent, I will continue to request thumbprints when I perform notarizations.  I’m confident that the majority of my clients will comply.

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