In two-phase sampling for stratification, the second-phase sample is selected by a stratified sample based on the information observed in the first-phase sample. We develop a replication-based bias adjusted variance estimator that extends the method of Kim, Navarro and Fuller (2006). The proposed method is also applicable when the first-phase sampling rate is not negligible and when second-phase sample selection is unequal probability Poisson sampling within each stratum. The proposed method can be extended to variance estimation for two-phase regression estimators. Results from a limited simulation study are presented