The monophyletic perspective on Lissamphibia's origin suggests it is a single, unified lineage stemming from a common ancestor, potentially within Lepospondyli as suggested by a 2011 study sampling extinct and living taxa. This supports a consistent evolutionary path with shared traits. Conversely, a polyphyletic perspective would imply that Lissamphibia evolved from multiple distinct lineages, which some suggest might include differing ancestors like temnospondyls, not reflecting a unitary group. The debate centers on anatomical and molecular data interpretations and congruency with fossil records .

The timing of lissamphibian diversification is debated due to varying interpretations of molecular phylogenetic data versus the paleontological record. One molecular study places the diversification around 330 million years ago, favoring the temnospondyl-origin hypothesis, while others argue it should be dated less than 300 million years ago based on calibration points more consistent with paleontological evidence. This debate involves calibrating molecular clocks to fossil evidence, complicating consensus on the lineage's origins .

Molecular and morphological data are crucial in resolving amphibian evolutionary history as they provide complementary evidence. Molecular phylogenetics help elucidate relationships between extant species by analyzing DNA sequences, while morphological data from fossils offer insights into physical and ecological adaptations over time. However, discrepancies between these data types occasionally arise, such as differing interpretations of phylogenetic branching points, necessitating careful calibration and integration to form coherent hypotheses about amphibian evolution .

Current frog lineages trace a significant diversification timing back to the Cretaceous–Paleogene extinction event, around 66 million years ago. Genetic studies suggest that several major families, such as Hyloidea and Microhylidae, along with the clade Natatanura, diversified simultaneously after this mass extinction event. This timing also coincides with a resurgence of forests, which contributed to adaptive radiations and arboreal lifestyles in these frog groups .

Evidence from Middle Jurassic fossils such as Notobatrachus degiustoi, which dated back 168-161 million years ago, suggests early frogs displayed adaptations for life in temporary aquatic environments. The adaptations for filter-feeding observed in their tadpoles imply they lived in temporary pools, a habitat that would require efficient feeding strategies due to fluctuating resource availability. This illustrates an early ecological niche as temporary pond dwellers .

Adaptations for jumping in early frogs evolved gradually from proto-frog species such as Triadobatrachus massinoti to early 'true frogs' like Prosalirus bitis. Over time, proto-frogs had separate tibia and fibula and retained tails. These constraints limited their leaping ability. In contrast, early frogs like Prosalirus showed morphological advancements such as fused long bones and reduced tails, reflecting an evolutionary pressure to enhance mobility, possibly driven by predatory threats or environmental factors such as habitat structure .

The discovery of 40-million-year-old helmeted frog fossils in Antarctica challenges previous assumptions about historical frog distribution and climates. This finding indicates that regions of Antarctica once supported forests similar to the Nothofagus forests of South America, providing habitats for frog species. It suggests significant paleoclimatic changes over millions of years and a wider historical geographic distribution of frogs than previously recognized .

The evolutionary change in chromosome numbers has occurred about 20 times faster in mammals than in frogs, leading to more rapid speciation in mammals. This suggests that while frogs have experienced considerable evolutionary success, their speciation and diversity have not relied as heavily on changes in ploidy as seen in mammal lineages. Frogs have instead diversified significantly after specific events like the Cretaceous–Paleogene extinction, whereas mammals show a broader, ongoing chromosomal evolution driving their speciation .

The discovery of Gerobatrachus hottoni, dated back 290 million years, contributes significantly to the understanding of amphibian evolutionary relationships as it is considered a missing link, exhibiting characteristics of both frogs and salamanders. This supports the hypothesis that these two groups (forming the clade Batrachia) are more closely related to each other than to caecilians . The implications of this finding rest on its potential position as a stem batrachian, providing a closer ancestor to the common ancestor of frogs and salamanders and enriching the discourse surrounding amphibian phylogeny .

Early proto-frogs like Triadobatrachus massinoti, which lived approximately 250 million years ago, have several key anatomical differences from modern frogs. Triadobatrachus had a longer body with more vertebrae, separate tail vertebrae unlike the fused urostyle in modern frogs, and separate tibia and fibula bones, indicating it was not adapted for efficient leaping. In contrast, modern frogs have a fused urostyle, fewer vertebrae, and elongated hind limbs adapted for jumping .