We define non-ordinary instanton bundles on Fano threefolds X extending the notion of (ordinary) instanton bundles introduced in [14]. We determine a lower bound for the quantum number of a non-ordinary instanton bundle, i.e. the degree of its second Chern class, showing the existence of such bundles for each admissible value of the quantum number when i X ≥ 2 or i X = 1 and rk Pic(X) = 1. In these cases we deal with the component inside the moduli spaces of simple bundles containing the vector bundles we construct and we study their restriction to lines. Finally we give a monadic description of non-ordinary instanton bundles on P 3 and the smooth quadric studying their loci of jumping lines, when of the expected codimension.