The eighth seed struggled throughout the contest before losing by a 6-2 7-5 scoreline to the world number 65.
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Makarova, a 2014 quarter-finalist at SW19, warmed up for this tournament with defeat to British number two Johanna Konta at Eastbourne, and she showed more signs of failing to adapt to the grass after dropping the opening set.
Rybarikova allowed her opponent just five points on her first serve, allowing her to break serve on three occasions to ease into the lead.
Makarova had a chance to break at the start of the second, but after Rybarikova survived, the set would progress to 5-5 before the 26-year-old broke serve again to secure an excellent win.