We resume the study initiated in [R. Crétois and L. Lang, The vanishing cycles of curves in toric surfaces, I, preprint (2017), arXiv:1701.00608]. For a generic curve [Formula: see text] in an ample linear system [Formula: see text] on a toric surface [Formula: see text], a vanishing cycle of [Formula: see text] is an isotopy class of simple closed curve that can be contracted to a point along a degeneration of [Formula: see text] to a nodal curve in [Formula: see text]. The obstructions that prevent a simple closed curve in [Formula: see text] from being a vanishing cycle are encoded by the adjoint line bundle [Formula: see text]. In this paper, we consider the linear systems carrying the two simplest types of obstruction. Geometrically, these obstructions manifest on [Formula: see text] respectively as an hyperelliptic involution and as a spin structure. In both cases, we determine all the vanishing cycles by investigating the associated monodromy maps, whose target space is the mapping class group [Formula: see text]. We show that the image of the monodromy is the subgroup of [Formula: see text] preserving respectively the hyperelliptic involution and the spin structure. The results obtained here support Conjecture [Formula: see text] in [R. Crétois and L. Lang, The vanishing cycles of curves in toric surfaces, I, preprint (2017), arXiv:1701.00608] aiming to describe all the vanishing cycles for any pair [Formula: see text].