PURPOSE: To investigate differences in sensitivity to myopia-inducing stimuli of two strains of pigmented guinea pigs. METHODS: Eleven-day-old animals (New Zealand [NZ], n = 24 and Elm Hill strains [EH], n = 26) wore either a +2 or -2 diopter (D) lens over one eye and a plano lens over the fellow eye for 5 days; other 10-day-old EH (n = 9) and 7-day-old NZ (n = 9) animals were monocularly form-deprived (FD) for 28 days. Choroidal thickness and axial length were measured using A-scan ultrasonography at baseline and after 1 and 5 days for optical defocus treatments, and at baseline and after 28 days for the FD treatment. Refractive errors were measured by retinoscopy. Choroids of untreated animals were also evaluated using spectral-domain optical coherence tomography. RESULTS: One day of optical defocus induced bidirectional (optical sign-dependent) choroidal responses in EH animals only (P < 0.01). Similar responses were detected in NZ animals after 5 days (P < 0.01), with concordant spherical equivalent refraction changes (P < 0.01). Compared with NZ animals, EH animals developed minimal myopia with FD after 28 days (-4.58 ± 0.97 vs. -0.69 ± 0.75 D for NZ versus EH, P < 0.001). Yet, EH animals showed paradoxical choroidal thickening, 20 ± 9 vs. -8 ± 8 μm for EH versus NZ, P < 0.001. Untreated EH animals also had significantly thicker choroids than NZ animals (147 ± 19 vs. 132 ± 16 μm, P < 0.05), with well-defined layering. CONCLUSIONS: As previously reported in chicks, guinea pigs show strain-related differences in response to myopia-inducing stimuli. The finding of a thicker, multilayered choroid in the strain showing decreased sensitivity to FD is provocative, suggesting a possible protective role of the choroid.