It says more than half of the anglers polled feared that the break-up of the Union would have an adverse impact on field sports tourism, which is worth some £240 million a year.
Nearly half of those polled said they were "very worried" or "slightly worried" by the prospect. But the Scottish Government dismissed it as unscientific and misinformed.
A total of 275 anglers responded from across the UK, Canada, Ireland, New Zealand, Norway, Russia and the US in research commissioned by Dundee sporting agent Salmo International.
They were asked: "Are you worried that if Scotland becomes an independent country, it could have a negative impact on salmon fishing and field sports tourism in general?
One-quarter said they were "very worried" and 28% "slightly worried". However, 38% claimed not to be worried.
Key causes of concern included increased investment in salmon farming (51%), changing government priorities (48%) and lack of enthusiasm for countryside issues (33%).
Salmo founder Greig Thomson said: "Emotions are running mighty high. While the good news is that our report reaffirmed Scotland's status as a world-class salmon fishing destination, the bad news is it uncovered serious worries about an unshackled government cosying up to the salmon farming industry at the expense of our wild salmon stocks.
"The overall consensus is that an independent Scotland wouldn't have the sport's interests at heart. This hammers home the message that the relentless pursuit of salmon farming comes not only with a significant ecological cost but also with financial pain due to diminished tourism income and the knock-on effect for communities."
A Scottish Government spokesman said: "This survey is highly unscientific and misinformed. The management of salmon fisheries is already fully devolved to Scotland.
"Under the present administration, the latest figures show that historic declines in salmon numbers returning to Scotland have been reversed, with rod catches for salmon in 2011 the sixth highest on record.
"We are fully committed to ensuring a viable, long-term future for both freshwater fisheries and fish farming, with effective management of interactions between the two sectors. That is why we have consulted on new legislation, with plans to introduce the Aquaculture and Fisheries Bill to Parliament in the autumn."
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