We report on a search for B(s)(0)->mu(+)mu(-) and B(d)(0)->mu(+)mu(-) decays in p (p) over bar collisions at root s=1.96 TeV using 364 pb(-1) of data collected by the CDF II detector at the Fermilab Tevatron Collider. After applying all selection requirements, we observe no candidates inside the B(s)(0) or B(d)(0) mass windows. The resulting upper limits on the branching fractions are B(B(s)(0)->mu(+)mu(-))< 1.5x10(-7) and B(B(d)(0)->mu(+)mu(-))< 3.9x10(-8) at 90% confidence level.