The Justice Department is suing Microsoft. The Federal Trade Commission is investigating Intel. Twenty state attorneys general are also suing Microsoft. Nineteen-hundred college assistant coaches are suing the NCAA. The American Booksellers Association is suing Barnes & Noble and Borders. All for antitrust. Without getting into the merits of antitrust policy in general or any particular case, who's in charge of making that policy?
Answer: all of the above. The FTC and Department of Justice have concurrent jurisdiction, meaning that both are supposed to chase antitrust violators. The two agencies divvy up cases to avoid duplicate investigations. A merger review is assigned to the agency best acquainted with that industry; a nonmerger investigation generally goes to the first agency that proposes it.
The courts often hold that aspects of national economic policy are "pre-empted" by the federal government under the Commerce Clause of the Constitution. The insight behind the Commerce Clause was precisely that a national economy can be harmed by duplicative and/or conflicting state regulations. Federal statutes often explicitly tell the states to keep out. But states may write and enforce their own antitrust law even, says the Supreme Court, if it contradicts federal law. State attorneys general may also sue in federal courts using federal law. Often state and federal agencies investigate and prosecute together, as in the Microsoft case.
Finally, victimized individuals and firms may sue for damages, under state and/or federal law. Federal law and some state laws award triple damages plus legal costs if you win.