Chlorites formed as a replacement of phenocrysts in metabasites from the pumpellyite-actinolite to lower-greenschist facies Mikabu and North Chichibu belts in southwest Japan were studied by X-ray powder diffraction, electron microprobe analysis (EMPA) and high-resolution transmission electron microscopy (HRTEM). The metabasites contain a small quantity of fine-grained smectite and corrensite in the <1 μm size fraction. The chlorite also contains trace amounts of Ca, Na and K, which generally appear to be associated with smectite stacked in chlorite packets. The smectite layers comprise up to 13% of the chlorite domains. Theoretical estimates of the smectite ratio by the Wise method using EMPA data coincide well with the ratio determined based on HRTEM observations in most chlorites. However, in some chlorites with high proportions of Ca, Na and K, the cations cannot be reasonably attributed to smectite alone. Based on the present analyses, Ca, Na and K cations are also hosted in discrete interstitial phases of fine-grained smectite and corrensite as possible retrograde metamorphic products. These findings suggest that care should be taken in application of the Wise method to estimate the smectite ratio, and that the whole-rock chlorite composition may not be suitable as a geothermometer.