flash player malware pop up in safari

Force Quit Safari ( command + option + esc keys).Then restart Safari holding the Shift key. 

Empty Caches (Safari menu > Preferences > Privacy > Remove all website data. (This will also remove history if you do not want to remove History open Safari Preferences > Advanced and check mark “Show Develop Menu” then choose “Empty Caches” from Develop Menu ).

Then go to Safari menu > Preferences > Extensions and check there. If there is an extension delete it.

Also check in System Preferences > Profiles (if you have that pane). If there's anything in there you don't recognize delete it.

If the problem persists then download and run Malwarebytes. Malwarebytes was developed by one of our own colleagues here in ASC and is about the most proven anti-malware software for Mac.

You're welcome. That's good news! In the future, only download Flash Player updates either from the Official Adobe Website or from with in System Preferences > Flash Player < Check for updates. All pop-ups telling you to download Flash will contain malware. Also FWIW, Adobe has announced they will stop supporting Flash Player this year. Since almost all websites now are HTML 5. it obviates the need for Flash.