user3624: To me, these tags are used almost interchangeably at the moment, and I think any attempt to separate them would be awkward. The tag wikis are almost circular as well, which is another indication that they overlap.
Wiki for mathematical-models:

Theoretical models that explain a system using mathematical equations. 

Wiki for theoretical-biology:

The modeling of biological processes using the tools of applied mathematics. 

My suggestion is to merge them, using theoretical-biology as the main tag, since this is a bit more general (could e.g. include non-formalized theoretical biology as well). I have already suggested this tag synonym, but not much has happened since the voting on tag synonyms is at a standstill.
I do see that there might/could be a slight difference in emphasis in these tags, where mathematical-models could be used in a more technical sense (any application using advanced mathematics) even if the focus isn't theoretical development of the subject. However, the current use do not match this and the number of questions that use these tags aren't that many. Therefore, I think it is more useful to merge them.
EDIT
In either case, and after seing the answer from @Corvus, I have now tried to separate the two tags by editing their tag wikis:

Theoretical biology
"Questions relating to biological theory or theoretical developments that deals with biological processes."
full wiki entry
Mathematical models"Models that analyse biological systems or processes using the tools
of applied mathematics."
full wiki entry

Please comment or edit if you don't find them suitable.

user13072: In principle, these are very different things. 
Plenty of theoretical biology contains little or no mathematics; the theory is verbal and conceptual.   R.A. Fisher's original model of why there is an even sex ratio provides just one of many examples of elegant work in this vein. George Williams's 1957 paper on the evolution of senescence does include a little model, but it is really tangential to the main thrust of the paper. What could be a greater theoretical breakthrough than Darwin's mathematics-free Origin of Species?  There's even a journal that focuses on this sort of thing: Biological Theory
Meanwhile, there is mathematical biology that is barely theoretical. Particularly in inference-heavy fields such as bioinformatics we find papers that make intense use of mathematics and/or statistics without advancing biological theory in the least. 
In practice, as the tags are used on this site, they do seem hard to separate. There may be a slight difference in focus: theoretical biology focusing on simple conceptual models while mathematical biology focuses on analytic and computational techniques. But maybe I'm just imagining things. In any event, I might suggest waiting to see if the distinctions start to sort themselves out. 

3624: <p>To me, these tags are used almost interchangeably at the moment, and I think any attempt to separate them would be awkward. The tag wikis are almost circular as well, which is another indication that they overlap.</p>

<p>Wiki for <a href="https://biology.stackexchange.com/questions/tagged/mathematical-models" class="post-tag" title="show questions tagged &#39;mathematical-models&#39;" rel="tag">mathematical-models</a>:</p>

<blockquote>
  <p>Theoretical models that explain a system using mathematical equations. </p>
</blockquote>

<p>Wiki for <a href="https://biology.stackexchange.com/questions/tagged/theoretical-biology" class="post-tag" title="show questions tagged &#39;theoretical-biology&#39;" rel="tag">theoretical-biology</a>:</p>

<blockquote>
  <p>The modeling of biological processes using the tools of applied mathematics. </p>
</blockquote>

<p>My suggestion is to merge them, using <a href="https://biology.stackexchange.com/questions/tagged/theoretical-biology" class="post-tag" title="show questions tagged &#39;theoretical-biology&#39;" rel="tag">theoretical-biology</a> as the main tag, since this is a bit more general (could e.g. include non-formalized theoretical biology as well). I have already <a href="https://biology.stackexchange.com/tags/theoretical-biology/synonyms">suggested this tag synonym</a>, but not much has happened since the voting on tag synonyms is at a standstill.</p>

<p>I do see that there might/could be a slight difference in emphasis in these tags, where <a href="https://biology.stackexchange.com/questions/tagged/mathematical-models" class="post-tag" title="show questions tagged &#39;mathematical-models&#39;" rel="tag">mathematical-models</a> could be used in a more technical sense (any application using advanced mathematics) even if the focus isn't theoretical development of the subject. However, the current use do not match this and the number of questions that use these tags aren't that many. Therefore, I think it is more useful to merge them.</p>

<p><strong>EDIT</strong></p>

<p>In either case, and after seing the answer from @Corvus, I have now tried to separate the two tags by editing their tag wikis:</p>

<ul>
<li><p>Theoretical biology<br>
"<em>Questions relating to biological theory or theoretical developments that deals with biological processes.</em>"<br>
<a href="https://biology.stackexchange.com/tags/theoretical-biology/info">full wiki entry</a></p></li>
<li><p>Mathematical models<br>"<em>Models that analyse biological systems or processes using the tools
of applied mathematics.</em>"<br>
<a href="https://biology.stackexchange.com/tags/mathematical-models/info">full wiki entry</a></p></li>
</ul>

<p>Please comment or edit if you don't find them suitable.</p>
 13072: <p>In principle, these are very different things. </p>

<p>Plenty of theoretical biology contains little or no mathematics; the theory is verbal and conceptual.   R.A. Fisher's original model of why there is an even sex ratio provides just one of many examples of elegant work in this vein. George Williams's 1957 paper on the evolution of senescence does include a little model, but it is really tangential to the main thrust of the paper. What could be a greater theoretical breakthrough than Darwin's mathematics-free <em>Origin of Species</em>?  There's even a journal that focuses on this sort of thing: <a href="http://www.springer.com/philosophy/epistemology+and+philosophy+of+science/journal/13752" rel="nofollow">Biological Theory</a></p>

<p>Meanwhile, there is mathematical biology that is barely theoretical. Particularly in inference-heavy fields such as bioinformatics we find papers that make intense use of mathematics and/or statistics without advancing biological theory in the least. </p>

<p>In practice, as the tags are used on this site, they do seem hard to separate. There may be a slight difference in focus: theoretical biology focusing on simple conceptual models while mathematical biology focuses on analytic and computational techniques. But maybe I'm just imagining things. In any event, I might suggest waiting to see if the distinctions start to sort themselves out. </p>
