Will the IRS accept two 1099s with the same tax ID number?

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Do you mean can your company issue two 1099s to the same vendor (same tax ID) for the same year?  No, the IRS wants you to issue one 1099, not two.  

If, on the other hand, a 1099 is issued by the organization that you acquired for payments it made to the vendor prior to acquisition, and your organization issued a 1099 to the same vendor for your payments excluding those of the acquired company made prior to the acquisition, that would be acceptable.

You may issue just one 1099 for the year covering all payments by both organizations, provided the requirements noted are met.

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