Apple’s iPod shuffle has now captured 58 percent of the flash memory-based audio player market, according to NPD data cited by Apple CFO Peter Oppenheimer in a meeting with Merrill Lynch analyst Steven Milunovich. The number is up from 43 percent share in February.

In a research note to clients obtained by iLounge, Milunovich said Apple isn’t concerned about mobile phones gaining more music capabilities. “Management argued that iPod will remain the best way to manage and listen to music with MP3 capability in handsets more complementary than a replacement,” he said. “The negatives of music on a handset include a worse user interface and limited battery life. Mr. Oppenheimer said he ‘doesn’t foresee problems working with carriers,’ implying that negotiating shared economics wouldn’t be a deal killer.”

Interestingly, Milunovich also said he expects wireless and video features in iPods for the holidays. “Our guess is that iPod will run short video clips, such as Britney Spears gyrating while ‘Toxic’ plays,” he said.