With many riders opting for a road bike over a time trial bike on the wet, undulating roads there were some surprising times recorded by the pre-stage favourites.
Izagirre completed the 3.95km course in 5-33 having trailed Lotto-Soudal's Louis Vervaecke by just a second at the halfway mark.
Show us your Scars: Geraint Thomas
General classification favourite Chris Froome was 26 seconds down on Izagirre, 10 seconds slower than rival Nairo Quintana. Tejay van Garderen is perhaps the best placed of the GC riders, finishing 11 seconds down.
One of the pre-stage favourites, Bob Jungels finished 24 seconds behind Izagirre on the technical course, made even tougher by the snowy conditions.
Orica-GreenEdge's Michael Albasini fell on a sharp downhill corner, but recovered to finish 36 seconds down.
Tour de Romandie prologue, La Chaux-de-Fonds (3.95km ITT)
1. Ion Izagirre (Esp) Movistar, 5-33
2. Tom Dumoulin (Ned) Giant-Alpecin, at 6s
3. Michal Kwiatkowski (Pol) Team Sky, at 7s
4. Geraint Thomas (GBr) Team Sky, st
5. Gorka Izagirre (Esp) Movistar, at 8s
6. Moreno Moser (Ita) Cannondale, at 9s
7. Reto Hollenstein (Swi) IAM Cycling, at 11s
8. Louis Vervaecke (Bel) Lotto-Soudal, st
9. Tejay van Garderen (USA) BMC, st
10. Martijn Keizer (Ned) LottoNL-Jumbo, at 12s
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