We investigate the phenomenology of a model based on the SU(3)_c× SU(3)_L× U(1)_X gauge theory, the so-called 331 model. In particular, we focus on the Higgs sector of the model which is composed of three SU(3)_L triplet Higgs fields, and this corresponds to the minimal form to realize phenomenologically acceptable scenario. After the spontaneous symmetry breaking SU(3)_L× U(1)_X→ SU(2)_L× U(1)_Y, our Higgs sector effectively becomes that with two SU(2)_L doublet scalar fields, in which the

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... t and the second generation quarks couple to the different Higgs doublet from that couples to the third generation quarks. This structure causes the flavour changing neutral current mediated by Higgs bosons at the tree level. By taking an alignment limit of the mass matrix for the CP-even Higgs bosons, which is naturally realized in the case with the breaking scale of SU(3)_L× U(1)_X to be much larger than that of SU(2)_L× U(1)_Y, we can avoid current constraints from flavour experiments such as the B^0-B̅^0 mixing even for the Higgs bosons masses being O(100) GeV. In this allowed parameter space, we clarify that a characteristic deviation in quark Yukawa couplings of the standard model-like Higgs boson is predicted, which has a different pattern from that seen in two Higgs doublet models with a softly-broken Z_2 symmetry. We also find that the flavour violating decay modes of the extra Higgs boson, e.g., H/A → tc and H^±→ ts can be dominant, and they yield the important signature to distinguish our model from the two Higgs doublet models.