We study the indirect detection of dark matter through neutrino flux from their annihilation in the center of the Sun, in a class of theories where the dark matter-nucleon spin-independent interactions break the isospin symmetry. We point out that, while the direct detection bounds with heavy targets like Xenon are weakened and reconciled with the positive signals in DAMA and CoGeNT experiments, the indirect detection using neutrino telescopes can impose a relatively stronger constraint and brings tension to such explanation, if the annihilation is dominated by heavy quark or $tau$-lepton final states. As a consequence, the qualified isospin violating dark matter candidate has to preferably annihilate into light flavors.