Spilogale pygmaea inhabits deciduous tropical forest, semi-evergreen forest, and desert scrub (Ceballos and Miranda 1986). One specimen was obtained in coastal sand dunes with only herbaceous vegetation cover (López-Forment and Urbano 1979). Most individuals have been found in undisturbed habitats and den use suggests that they still are dependent on forests (Cantú-Salazar et al. 2009). Altitudinal distribution is usually 0-100 m above sea level (Van Gelder 1959), with records up to 1,630 m a.s.l. The mean home range was 20.4 ha, with male home ranges larger than those of females (Cantú-Salazar et al. 1999). Spilogale pygmaea is nocturnal. It makes its dens underground or in fallen logs, among rocks, or simply under dense vegetation cover. Food consists of insects, spiders, birds, eggs, small mammals, and some fruit and seeds (Ceballos and Miranda 1986).

Pygmy Spotted Skunk is endemic to the tropical Pacific Coast of Mexico, from Sinaloa south to Oaxaca (Medellín et al. 1998). The species is found from sea-level up to 1630 m asl, but is most common below 350 m.

The species is considered 'vulnerable' (Ceballos and Navarro 1991) and has been listed since 1994 as 'threatened' by the federal governnent of Mexico (2010). Its presence in protected areas has been confirmed in the Cuixmala Biosphere reserve in the coast of Jalisco (Medellín et al. 1998).