Using Microwell-seq, we analyzed more than 500,000 single cells covering all major Xenopus tissues to construct the first Xenopus cell landscape to date. Common cell lineage-specific transcription factors have been identified in vertebrates, including fish, amphibians and mammals. A comparison of larval and adult erythrocytes revealed larval and adult-specific hemoglobin subtypes and a cluster of erythrocytes containing both larval and adult hemoglobin, mainly at NF59. In addition, cell lineages originating from all three layers exhibited both antigen processing and presentation during metamorphosis, indicating a common regulatory mechanism in metamorphosis. Our study provides a comprehensive resource for research on Xenopus developmental biology.