Speciation in generative diffusion models denotes the emergence of distinct stable branches during denoising, through which initially undifferentiated trajectories progressively commit to different data classes. In this work we develop an intrinsic theory of speciation for diffusion models supported on compact Riemannian manifolds: the aim is to go beyond existing theoretical descriptions, which usually identify speciation with a symmetric pitchfork bifurcation and assume to work in a large-dimensional space. We characterize speciation by bifurcations of the critical points of the evolving probability density. A spectral heat-kernel representation makes explicit the role of the manifold geometry, while Poincaré-Hopf and Morse theory impose global constraints on the number and type of score equilibria and reveal topologically-imposed geometrical modes. For mixtures of heat kernels, we prove that generic speciation events have a one-dimensional critical kernel and admit an A2 fold normal form; pitchforks and simultaneous multidirectional transitions arise from nongeneric symmetric configurations. We derive geometry-dependent estimates of speciation times for bimodal mixtures and Riemannian regular simplices. We further establish structural stability of nondegenerate folds under score perturbations and show that the first-order time shift is determined solely by the component of the score error along the critical direction. The theory is illustrated on the sphere using mixtures of von Mises-Fisher distributions, where pitchfork and saddle-node bifurcations, topological modes, and hierarchical multiple speciations are observed. Finally, a chart-based intrinsic score-learning scheme based on neural networks contrasts the theoretically predicted transitions on prototypal and more complex datasets.

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