Dark pools in crosshairs after Barclays charges

While the complaint doesn't necessarily get at the fabric of dark pools, it is likely to raise questions about the need for transparency at a time when the Securities and Exchange Commission and other regulators have taken dead aim at cleaning up the trading climate.

Dark pool trading happens away from major exchanges like the Nasdaq or New York Stock Exchange and does not have to be reported publicly. It is responsible for about 40 percent of all stock trading and is used often by high-frequency traders.

Read MoreBarclays launches internal dark pool investigation

The regulatory climate generally has seen SEC Chair Mary Jo White pledge changes to HFT rules for later in the year. In May, the New York Stock Exchange paid a $4.5 million penalty to resolve HFT-related charges the commission brought, and a slew of other parties have had to pay penalties in cases related to trading irregularities.

"Right now it's isolated at Barclays. The case reads like more of a marketing fraud situation as opposed to what was actually going on inside of the dark pool," Saluzzi said. "But it's the first time a dark pool has been kind of dinged."

How far the efforts go to reform dark pools likely will depend on how much Washington regulators are willing to anger Wall Street.

Read MoreBanks withdraw from Barclays' dark pool -FT

The SEC, in fact, already has a set of proposed changes at the readya 116-page document prepared in 2009 called the "Regulation of Non-Public Trading Interest."

There were three broad recommendations made: Changing the definition of "bid" and "offer" to express "actionable indications of interest" rather than quotes that were never meant to be executed; a "substantial lowering of the trading volume" benchmarks for dark pools before they had to release consolidated trading data; and changing rules that would provide for the "real-time disclosure of the identify of dark pools and other (alternative trading systems) on the reports of their executed trades."

"The proposals are intended to promote the Exchange Act goals of transparency, fairness, and efficiency," the document stated.

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Dark pools in crosshairs after Barclays charges