We establish necessary and sufficient conditions for a semigroup identity to hold in the monoid of $n\times n$ upper triangular tropical matrices, in terms of equivalence of certain tropical polynomials. This leads to an algorithm for checking whether such an identity holds, in time polynomial in the length of the identity and size of the alphabet. It also allows us to answer a question of Izhakian and Margolis, by showing that the identities which hold in the monoid of $2\times 2$ upper triangular tropical matrices are exactly the same as those which hold in the bicyclic monoid. Our results extend to a broader class of "chain structured tropical matrix semigroups"; we exhibit a faithful representation of the free monogenic inverse semigroup within such a semigroup, which leads also to a representation by $3\times 3$ upper triangular matrix semigroups, and a new proof of the fact that this semigroup satisfies the same identities as the bicyclic monoid.

21 pages. This amended version of the author accepted manuscript contains a corrected proof of Proposition 7.1. The new proof establishes the proposition exactly as originally published, all other results are unaffected and the manuscript is otherwise unamended