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You don't have to collect it if they are an affiliate program based in the US. If they are based in Canada, then technically you are supposed to collect it from the sponsor when you receive your affiliate commissions. Some supposedly will pay this to you if you ask them, otherwise you just have to pay it out of your own pocket.
This is from their site:
Example
A non-resident person who is not registered for GST/HST purposes pays a fee to a registered Canadian
Web site owner to place banner ads for its business on the Web site.
The Canadian Web site owner is not required to collect the GST/HST on the fee, as the supply to the
non-resident is an advertising service that is zero-rated under section 8 of Part V of Schedule VI.
replace the XXX with www
XXX.cra-arc.gc.ca/E/pub/gm/b-090/b-090-e.pdf
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