Yes, you can use MCMC in ecological studies. For example, see the paper below, which uses a Monte Carlo Markov Chain algorithm for estimating a subset of the parameters in a seven compartment ecosystem model.
Article A Markov chain Monte Carlo method for estimation and assimil...
MCMC can be considered in making sampling decision towards conservation of animals but the method can be improved upon to increase computation efficiency while reducing time.
Kindly see: Turek et al. (2016). Efficient Markov Chain Monte Carlo Sampling for Hierarchical Hidden Markov Models ... https://arxiv.org/pdf/1601.02698.pdf
Also this article by Link et al. (2002). Of Bugs and Birds: Markov Chain Monte Carlo for Hierarchical Modeling in Wildlife Research ... provides an application of the method in wildlife conservation. http://canuck.dnr.cornell.edu/research/pubs/pdf/MCMC_JWM.pdf
MCMC can be used for that. There are some interesting books that discuss MCMC applications for Ecology related problems, for example; Kery's Introduction to WinBUGS for Ecologists: Bayesian Approach to Regression, ANOVA, Mixed Models and Related Analyses could be a good catch for you.