Cultural Ecosystem Services (CES) are non-material benefits that are indispensable for the health and well-being of communities. CES are often spatially explicit and fluctuate according to the knowledge, beliefs, and perception of users of the location. Therefore, understanding the spatial patterns of CES perceived by people from different backgrounds is important for decision-makers to carry out proactive landscape planning. In this study, we investigated the differences in the perception of CES between residents and tourists on Ishigaki Island, Japan. The study employed a Public Participation Geographic Information System (PPGIS) approach to spatially present the respective perceptions of residents and tourists regarding six types of CES, namely recreational, therapeutic, educational, spiritual, aesthetic, and historic CES, that are recognized as key contributors to human health and well-being. For data collection, we employed a combination of household-level postal surveys and in-person questionnaire surveys targeting residents (n = 410) and tourists (n = 102), respectively. A series of statistical and spatial analyses was conducted on the survey results to understand the influence of the duration of residence and the frequency of visits in shaping the perceptions of CES, as well as the relationship between perceived CES and land-use types. This included the contribution of protected areas to the delivery of CES. The results showed that the average number of locations indicated by residents was significantly higher than that indicated by the tourists, resulting in density maps with distinct spatial patterns. In particular, the spatial pattern of CES identified by tourists was considerably simpler than that recognized by residents and centered on two popular tourist spots. As per the elements of landscapes and seascapes, the perception of “aesthetic,” “recreational,” “therapeutic,” and “educational” CES by residents was associated with “forest” and “sea” and that of “spiritual” and “historic” was associated with “forest” and “farmland.” In contrast, the CES perception of “recreational,” “educational,” “therapeutic,” “aesthetic,” and “historic” by tourists was associated with “sea” and “forest.” “Spiritual” CES was associated with “forest” and “sea.” Lastly, a higher proportion of “aesthetic” CES locations were identified within protected areas compared to outside the areas. Overall, our findings revealed that residents and tourists perceive and appreciate the numerous CES arising from landscapes and seascapes of the island differently. This indicates a possible trade-off resulting from land or sea developments to the benefit among stakeholders, for example, tourists. Hence, to sustain CES that underpin equitable health and well-being benefits, spatial planning should consider the different perceptions of stakeholders, particularly of residents and tourists, regarding CES types and locations.