Abstract We derive the most general expression for the Skyrmion topological charge for a two-dimensional spin texture, valid for any type of boundary conditions or for any arbitrary spatial region within the texture. It reduces to the usual one for the appropriate boundary conditions. The general expression resembles the Gauss-Bonet theorem for the Euler-Poincaré characteristic of a 2D surface, but it has definite differences, responsible for the assignment of the proper signs of the Skyrmion charges. Additionally, we show that the charge of a single Skyrmion is the product of the value of the normal component of the spin texture at the singularity times the Index or winding number of the transverse texture, a generalization of a Poincaré theorem. We illustrate our general results analyzing in detail a two-component spinor Bose–Einstein condensate (BEC) in 2D in the presence of an external magnetic field, via the Gross-Pitaevskii equation. The condensate spin textures present Skyrmions singularities at the spatial locations where the transverse magnetic field vanishes. We show that the ensuing superfluid vortices and Skyrmions have the same value for their corresponding topological charges, in turn due to the structure of the magnetic field.